Devoir 2 - Phylogénétique
Juliette Pourrain, Nesrine Imloul, Daniel Ilboudo, Nicolas Campeau, Jérôme Fortin
4 avril 2025
Jeu de données
Cytochrome oxidase I (COI), marqueur mitochondrial utilisé pour le DNA barcoding.
Taxons : Cétacés (Baleines), groupe frère des Cétacés : l’Hippopotame, groupe externe de (Cétacés + Hippopotame) : Pinnipèdes (groupe externe).
Installation package
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## Attachement du package : 'ape'## Les objets suivants sont masqués depuis 'package:seqinr':
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## as.alignment, consensus## Le chargement a nécessité le package : Biostrings## Le chargement a nécessité le package : BiocGenerics##
## Attachement du package : 'BiocGenerics'## Les objets suivants sont masqués depuis 'package:stats':
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## IQR, mad, sd, var, xtabs## Les objets suivants sont masqués depuis 'package:base':
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## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
## table, tapply, union, unique, unsplit, which.max, which.min## Le chargement a nécessité le package : S4Vectors## Le chargement a nécessité le package : stats4##
## Attachement du package : 'S4Vectors'## L'objet suivant est masqué depuis 'package:utils':
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## findMatches## Les objets suivants sont masqués depuis 'package:base':
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## expand.grid, I, unname## Le chargement a nécessité le package : IRanges## Le chargement a nécessité le package : XVector## Le chargement a nécessité le package : GenomeInfoDb##
## Attachement du package : 'Biostrings'## L'objet suivant est masqué depuis 'package:ape':
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## complement## L'objet suivant est masqué depuis 'package:seqinr':
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## translate## L'objet suivant est masqué depuis 'package:base':
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## strsplitA) Importer le jeu de séquences sur R, faire un alignement avec DECIPHER.
Utiliser les paramètres d’alignement par défaut, puis avec des pénalités de zéro pour l’ouverture d’indels (gaps) et leur prolongement.
Importer le jeu de sequence “Cetacea COI.txt”
# Conversion de .txt en format .fasta
mySequences <- readDNAStringSet("Cetacea COI.txt", format = "fasta")
# Garder juste les numeros ( GI Number) comme nom pour reduire la taille
names(mySequences) <- sub(".*?(\\d+).*", "\\1", names(mySequences))Paramètres défaut: Une pénalité entre 16 et 18 sur l’ouverture d’indels Et une pénalité entre 2 et 1 sur leur prolongement
# Aligner avec les paramètres par défaut
mySequences_align = AlignSeqs(mySequences, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 9-mers:
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## Realigning Sequences:
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## Time difference of 0.01 secs# Calcul des distances
mySequences_align_ape = as.DNAbin(mySequences_align)
mySequences_align_JC = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "JC69")
#Visualisation
plot(mySequences_align_JC, main = "Valeurs de distance entre les séquences par position nucléotidique pour l'alignement avec les paramètres par défaut.", ylab = "distance", xlab= "position")
Pénalités de zéro pour l’ouverture d’indels (gaps) et leur prolongement.
# Aligner avec les paramètres par défaut
mySequences_align_param_zero = AlignSeqs(mySequences, gapOpening = 0, gapExtension = 0 )## Determining distance matrix based on shared 9-mers:
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## Clustering into groups by similarity:
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## Reclustering into groups by similarity:
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## Refining the alignment:
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## Time difference of 0.17 secsmySequences_align_ape_param_zero = as.DNAbin(mySequences_align_param_zero)# Calcul des distances
mySequences_align_JC_param_zero = dist.dna(mySequences_align_ape_param_zero, pairwise.deletion = FALSE, model = "JC69")
#Visualisation
plot(mySequences_align_JC_param_zero, main = "Valeurs de distance entre les séquences par position nucléotidique", ylab = "distance", xlab= "position")
B) Faire un alignement en utilisant les séquences traduites en AA
i) Faire un alignement d’AA traduits à partir des séquences nucléotidiques en utilisant les paramètres par défaut d’alignement.
head(GENETIC_CODE_TABLE)## name
## 1 Standard
## 2 Vertebrate Mitochondrial
## 3 Yeast Mitochondrial
## 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
## 5 Invertebrate Mitochondrial
## 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
## name2 id AAs
## 1 SGC0 1 FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 2 SGC1 2 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
## 3 SGC2 3 FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 4 SGC3 4 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## 5 SGC4 5 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
## 6 SGC5 6 FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
## Starts
## 1 ---M---------------M---------------M----------------------------
## 2 --------------------------------MMMM---------------M------------
## 3 ----------------------------------MM----------------------------
## 4 --MM---------------M------------MMMM---------------M------------
## 5 ---M----------------------------MMMM---------------M------------
## 6 -----------------------------------M----------------------------Paramètres GeneticCode : 2 (Vertebrate Mitochondrial)
my_g_table <- getGeneticCode("2") ## Vertebrate Mitochondrial
mySequences_align_aa = AlignTranslation(
mySequences,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
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## Clustering into groups by similarity:
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## Alignment converged - skipping remaining iteration.ii) Tester un cadre de lecture différent de celui qui a été choisi par défaut.
Cadre de lecture 1:
mySequences_align_aa_cadre_1 = AlignTranslation(
mySequences,
sense = "+",
readingFrame = 1,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table) ## Determining distance matrix based on shared 5-mers:
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## Time difference of 0.01 secsC) Calcul des distances avec la librairie ape et optimisation du modèle avec bootstrap et modelTest
i) Utiliser l’alignement nucléotidique avec la librairie ape et produire les matrices de distances avec les modèles évolutifs suivants : Jukes et Cantor, Kimura 2 paramètres, Tamura et Nei, et le modèle de Galtier et Gouy.
# Conversion pour format ape
mySequences_align_ape = as.DNAbin(mySequences_align)Matrice de distances
# Jukes et Cantor
mySequences_align_JC = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "JC69")
# Kimura 2 paramètres
mySequences_align_K80 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "K80")
# Tamura et Nei
mySequences_align_TN93 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "TN93")
# Galtier et Gouy
mySequences_align_GG95 = dist.dna(mySequences_align_ape, pairwise.deletion = FALSE, model = "GG95") Visualisations
plot(mySequences_align_JC, main = "Valeurs de distance entre les séquences par position nucléotidique pour Jukes et Cantor", ylab = "distance", xlab= "position")
plot(mySequences_align_K80, main = "Valeurs de distance entre les séquences par position nucléotidique pour Kimura 2 paramètres", ylab = "distance", xlab= "position")
plot(mySequences_align_TN93, main = "Valeurs de distance entre les séquences par position nucléotidique pour Tamura et Nei", ylab = "distance", xlab= "position")
plot(mySequences_align_GG95, main = "Valeurs de distance entre les séquences par position nucléotidique pour Galtier et Gouy", ylab = "distance", xlab= "position")
ii) Faire une analyse de « bootstrap » avec 1000 itérations pour chaque modèle (Neighbor-Joining).
Construction d’arbres avec le Neighbor-Joining
mySequences_align_JC_NJ = nj(mySequences_align_JC)
mySequences_align_K80_NJ = nj(mySequences_align_K80)
mySequences_align_TN93_NJ = nj(mySequences_align_TN93)
mySequences_align_GG95_NJ = nj(mySequences_align_GG95)Arbres phylogénétiques
plot(mySequences_align_JC_NJ, main="Jukes et Cantor")
plot(mySequences_align_K80_NJ, main="Kimura 2 parametres 1980")
plot(mySequences_align_TN93_NJ, main="Tamura et Nei 1993")
plot(mySequences_align_GG95_NJ, main="Galtier and Gouy 1995")
Comparaison des modèles entre eux par corrélation (Pearson)
round(cor(cbind(mySequences_align_JC,mySequences_align_TN93,mySequences_align_K80, mySequences_align_GG95)),3)## mySequences_align_JC mySequences_align_TN93
## mySequences_align_JC 1.000 0.998
## mySequences_align_TN93 0.998 1.000
## mySequences_align_K80 0.999 0.999
## mySequences_align_GG95 0.866 0.840
## mySequences_align_K80 mySequences_align_GG95
## mySequences_align_JC 0.999 0.866
## mySequences_align_TN93 0.999 0.840
## mySequences_align_K80 1.000 0.850
## mySequences_align_GG95 0.850 1.000Analyse Bootstrap
mySequences_align_JC_NJ_boot = boot.phylo(phy = mySequences_align_JC_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "JC69")), B = 1000)## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.mySequences_align_TN_NJ_boot = boot.phylo(phy = mySequences_align_TN93_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "TN93")), B = 1000)## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.mySequences_align_K80_NJ_boot = boot.phylo(phy = mySequences_align_K80_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "K80")), B = 1000)## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.mySequences_align_GG95_NJ_boot = boot.phylo(phy = mySequences_align_GG95_NJ, x = as.matrix(mySequences_align_ape), FUN = function(xx) nj(dist.dna(xx,pairwise.deletion = FALSE, model = "GG95")), B = 1000)## Running bootstraps: 100 / 1000Running bootstraps: 200 / 1000Running bootstraps: 300 / 1000Running bootstraps: 400 / 1000Running bootstraps: 500 / 1000Running bootstraps: 600 / 1000Running bootstraps: 700 / 1000Running bootstraps: 800 / 1000Running bootstraps: 900 / 1000Running bootstraps: 1000 / 1000
## Calculating bootstrap values... done.Arbres Bootstrap
plot(mySequences_align_JC_NJ, main = "Jukes et Cantor", no.margin = TRUE)
nodelabels(mySequences_align_JC_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_TN93_NJ, main = "Tamura et Nei 1993", no.margin = TRUE)
nodelabels(mySequences_align_TN_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_K80_NJ, main = "Kimura 2 parametres 1980", no.margin = TRUE)
nodelabels(mySequences_align_K80_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
plot(mySequences_align_GG95_NJ, main = "GG95", no.margin = TRUE)
nodelabels(mySequences_align_GG95_NJ_boot/10, bg = "white", frame = "circle", cex = 0.6)
iii) Rechercher quel modèle maximise la robustesse (score maximum de bootstrap aux différents noeuds) de chaque arbre.
Comparaison des Bootstraps
#Enlever les NA pour ne pas avoir d'erreur
mySequences_align_JC_NJ_boot <- na.omit(mySequences_align_JC_NJ_boot)
mySequences_align_TN_NJ_boot <- na.omit(mySequences_align_TN_NJ_boot)
mySequences_align_K80_NJ_boot <- na.omit(mySequences_align_K80_NJ_boot)
mySequences_align_GG95_NJ_boot <- na.omit(mySequences_align_GG95_NJ_boot)
round(cor(cbind(mySequences_align_JC_NJ_boot,mySequences_align_TN_NJ_boot,mySequences_align_K80_NJ_boot, mySequences_align_GG95_NJ_boot)),3)## mySequences_align_JC_NJ_boot
## mySequences_align_JC_NJ_boot 1.000
## mySequences_align_TN_NJ_boot 0.634
## mySequences_align_K80_NJ_boot 0.675
## mySequences_align_GG95_NJ_boot 0.238
## mySequences_align_TN_NJ_boot
## mySequences_align_JC_NJ_boot 0.634
## mySequences_align_TN_NJ_boot 1.000
## mySequences_align_K80_NJ_boot 0.818
## mySequences_align_GG95_NJ_boot 0.603
## mySequences_align_K80_NJ_boot
## mySequences_align_JC_NJ_boot 0.675
## mySequences_align_TN_NJ_boot 0.818
## mySequences_align_K80_NJ_boot 1.000
## mySequences_align_GG95_NJ_boot 0.458
## mySequences_align_GG95_NJ_boot
## mySequences_align_JC_NJ_boot 0.238
## mySequences_align_TN_NJ_boot 0.603
## mySequences_align_K80_NJ_boot 0.458
## mySequences_align_GG95_NJ_boot 1.000iv) Passage à phangorn, utiliser la fonction modelTest() afin de rechercher le meilleur modèle. Si le modèle implique les paramètres gamma et/ou I (sites invariants), extraire la/les valeurs pour chaque paramètre.
Rechercher le meilleur modèle
mySequences_phangorn = as.phyDat(mySequences_align_ape)
mySequences_modelTest = phangorn::modelTest(mySequences_phangorn)## Model df logLik AIC BIC
## JC 61 -6699.334 13520.67 13846.62
## JC+I 62 -6343.549 12811.1 13142.39
## JC+G(4) 62 -6353.09 12830.18 13161.47
## JC+G(4)+I 63 -6340.357 12806.71 13143.35
## F81 64 -6638.961 13405.92 13747.9
## F81+I 65 -6267.654 12665.31 13012.63
## F81+G(4) 65 -6275.782 12681.56 13028.89
## F81+G(4)+I 66 -6263.407 12658.81 13011.48
## K80 62 -6335.641 12795.28 13126.57
## K80+I 63 -5925.895 11977.79 12314.43
## K80+G(4) 63 -5917.566 11961.13 12297.77
## K80+G(4)+I 64 -5910.923 11949.85 12291.82
## HKY 65 -6276.194 12682.39 13029.71
## HKY+I 66 -5834.262 11800.52 12153.19
## HKY+G(4) 66 -5830.95 11793.9 12146.57
## HKY+G(4)+I 67 -5823.406 11780.81 12138.82
## TrNe 63 -6296.975 12719.95 13056.59
## TrNe+I 64 -5887.889 11903.78 12245.76
## TrNe+G(4) 64 -5890.955 11909.91 12251.89
## TrNe+G(4)+I 65 -5877.541 11885.08 12232.41
## TrN 66 -6263.725 12659.45 13012.12
## TrN+I 67 -5829.366 11792.73 12150.74
## TrN+G(4) 67 -5827.718 11789.44 12147.45
## TrN+G(4)+I 68 -5818.456 11772.91 12136.27
## TPM1 63 -6335.602 12797.2 13133.84
## TPM1+I 64 -5925.7 11979.4 12321.38
## TPM1+G(4) 64 -5917.427 11962.85 12304.83
## TPM1+G(4)+I 65 -5910.598 11951.2 12298.52
## K81 63 -6335.602 12797.2 13133.84
## K81+I 64 -5925.7 11979.4 12321.38
## K81+G(4) 64 -5917.427 11962.85 12304.83
## K81+G(4)+I 65 -5910.598 11951.2 12298.52
## TPM1u 66 -6276.094 12684.19 13036.85
## TPM1u+I 67 -5833.82 11801.64 12159.65
## TPM1u+G(4) 67 -5830.683 11795.37 12153.38
## TPM1u+G(4)+I 68 -5822.876 11781.75 12145.11
## TPM2 63 -6275.356 12676.71 13013.35
## TPM2+I 64 -5900.296 11928.59 12270.57
## TPM2+G(4) 64 -5889.941 11907.88 12249.86
## TPM2+G(4)+I 65 -5881.346 11892.69 12240.01
## TPM2u 66 -6234.278 12600.56 12953.22
## TPM2u+I 67 -5824.232 11782.46 12140.47
## TPM2u+G(4) 67 -5821.934 11777.87 12135.88
## TPM2u+G(4)+I 68 -5812.364 11760.73 12124.08
## TPM3 63 -6335.582 12797.16 13133.8
## TPM3+I 64 -5922.373 11972.75 12314.73
## TPM3+G(4) 64 -5915.104 11958.21 12300.19
## TPM3+G(4)+I 65 -5907.827 11945.65 12292.98
## TPM3u 66 -6276.022 12684.04 13036.71
## TPM3u+I 67 -5830.507 11795.01 12153.02
## TPM3u+G(4) 67 -5828.685 11791.37 12149.38
## TPM3u+G(4)+I 68 -5820.253 11776.51 12139.86
## TIM1e 64 -6296.938 12721.88 13063.86
## TIM1e+I 65 -5887.793 11905.59 12252.91
## TIM1e+G(4) 65 -5890.803 11911.61 12258.93
## TIM1e+G(4)+I 66 -5877.297 11886.59 12239.26
## TIM1 67 -6263.631 12661.26 13019.27
## TIM1+I 68 -5828.973 11793.95 12157.3
## TIM1+G(4) 68 -5827.429 11790.86 12154.21
## TIM1+G(4)+I 69 -5817.935 11773.87 12142.57
## TIM2e 64 -6237.587 12603.17 12945.15
## TIM2e+I 65 -5853.553 11837.11 12184.43
## TIM2e+G(4) 65 -5859.192 11848.38 12195.71
## TIM2e+G(4)+I 66 -5843.839 11819.68 12172.34
## TIM2 67 -6222.408 12578.82 12936.83
## TIM2+I 68 -5816.425 11768.85 12132.2
## TIM2+G(4) 68 -5816.814 11769.63 12132.98
## TIM2+G(4)+I 69 -5805.14 11748.28 12116.98
## TIM3e 64 -6296.937 12721.87 13063.85
## TIM3e+I 65 -5883.586 11897.17 12244.49
## TIM3e+G(4) 65 -5888.332 11906.66 12253.99
## TIM3e+G(4)+I 66 -5873.437 11878.87 12231.54
## TIM3 67 -6263.573 12661.15 13019.16
## TIM3+I 68 -5825.501 11787 12150.36
## TIM3+G(4) 68 -5825.397 11786.79 12150.15
## TIM3+G(4)+I 69 -5814.993 11767.99 12136.68
## TVMe 65 -6275.16 12680.32 13027.64
## TVMe+I 66 -5896.951 11925.9 12278.57
## TVMe+G(4) 66 -5887.499 11907 12259.66
## TVMe+G(4)+I 67 -5878.736 11891.47 12249.48
## TVM 68 -6233.969 12603.94 12967.29
## TVM+I 69 -5820.188 11778.38 12147.07
## TVM+G(4) 69 -5819.268 11776.54 12145.23
## TVM+G(4)+I 70 -5808.999 11758 12132.04
## SYM 66 -6237.48 12606.96 12959.63
## SYM+I 67 -5848.96 11831.92 12189.93
## SYM+G(4) 67 -5856.016 11846.03 12204.04
## SYM+G(4)+I 68 -5839.587 11815.17 12178.53
## GTR 69 -6222.154 12582.31 12951
## GTR+I 70 -5812.051 11764.1 12138.14
## GTR+G(4) 70 -5813.937 11767.87 12141.91
## GTR+G(4)+I 71 -5801.327 11744.65 12124.04env <- attr(mySequences_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"#Meilleur modele avec les parametre AIC et BIC.
mySequences_modelTest[order(mySequences_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 71 -5801.327 11744.65 8.585027e-01 11751.59 8.330917e-01
## 68 TIM2+G(4)+I 69 -5805.140 11748.28 1.400575e-01 11754.82 1.653002e-01
## 84 TVM+G(4)+I 70 -5808.999 11758.00 1.086518e-03 11764.74 1.163642e-03
## 44 TPM2u+G(4)+I 68 -5812.364 11760.73 2.774303e-04 11767.08 3.602968e-04
## 90 GTR+I 70 -5812.051 11764.10 5.133160e-05 11770.84 5.497525e-05
## 91 GTR+G(4) 70 -5813.937 11767.87 7.784852e-06 11774.61 8.337440e-06
## 76 TIM3+G(4)+I 69 -5814.993 11767.99 7.362056e-06 11774.53 8.688927e-06
## 66 TIM2+I 68 -5816.425 11768.85 4.780728e-06 11775.20 6.208698e-06
## 67 TIM2+G(4) 68 -5816.814 11769.63 3.239588e-06 11775.98 4.207231e-06
## 24 TrN+G(4)+I 68 -5818.456 11772.91 6.269809e-07 11779.27 8.142557e-07
## 60 TIM1+G(4)+I 69 -5817.935 11773.87 3.886606e-07 11780.41 4.587093e-07
## 52 TPM3u+G(4)+I 68 -5820.253 11776.51 1.039606e-07 11782.86 1.350129e-07
## 83 TVM+G(4) 69 -5819.268 11776.54 1.024807e-07 11783.08 1.209509e-07
## 43 TPM2u+G(4) 67 -5821.934 11777.87 5.260518e-08 11784.03 7.506381e-08
## 82 TVM+I 69 -5820.188 11778.38 4.083387e-08 11784.92 4.819340e-08
## 16 HKY+G(4)+I 67 -5823.406 11780.81 1.208125e-08 11786.98 1.723908e-08
## 36 TPM1u+G(4)+I 68 -5822.876 11781.75 7.545176e-09 11788.11 9.798867e-09
## 42 TPM2u+I 67 -5824.232 11782.46 5.287646e-09 11788.63 7.545090e-09
## 75 TIM3+G(4) 68 -5825.397 11786.79 6.068114e-10 11793.15 7.880617e-10
## 74 TIM3+I 68 -5825.501 11787.00 5.465109e-10 11793.36 7.097499e-10
## 23 TrN+G(4) 67 -5827.718 11789.44 1.619205e-10 11795.60 2.310489e-10
## 59 TIM1+G(4) 68 -5827.429 11790.86 7.955656e-11 11797.21 1.033195e-10
## 51 TPM3u+G(4) 67 -5828.685 11791.37 6.155710e-11 11797.54 8.783756e-11
## 22 TrN+I 67 -5829.366 11792.73 3.114656e-11 11798.90 4.444390e-11
## 15 HKY+G(4) 66 -5830.950 11793.90 1.738266e-11 11799.88 2.721267e-11
## 58 TIM1+I 68 -5828.973 11793.95 1.698083e-11 11800.30 2.205289e-11
## 50 TPM3u+I 67 -5830.507 11795.01 9.954726e-12 11801.18 1.420468e-11
## 35 TPM1u+G(4) 67 -5830.683 11795.37 8.345047e-12 11801.53 1.190778e-11
## 14 HKY+I 66 -5834.262 11800.52 6.333259e-13 11806.50 9.914763e-13
## 34 TPM1u+I 67 -5833.820 11801.64 3.622694e-13 11807.81 5.169324e-13
## 88 SYM+G(4)+I 68 -5839.587 11815.17 4.172462e-16 11821.53 5.418747e-16
## 64 TIM2e+G(4)+I 66 -5843.839 11819.68 4.386452e-17 11825.66 6.867023e-17
## 86 SYM+I 67 -5848.960 11831.92 9.635430e-20 11838.09 1.374907e-19
## 62 TIM2e+I 65 -5853.553 11837.11 7.205475e-21 11842.90 1.235747e-20
## 87 SYM+G(4) 67 -5856.016 11846.03 8.311607e-23 11852.20 1.186007e-22
## 63 TIM2e+G(4) 65 -5859.192 11848.38 2.563529e-23 11854.18 4.396479e-23
## 72 TIM3e+G(4)+I 66 -5873.437 11878.87 6.141221e-30 11884.85 9.614126e-30
## 20 TrNe+G(4)+I 65 -5877.541 11885.08 2.752968e-31 11890.88 4.721370e-31
## 56 TIM1e+G(4)+I 66 -5877.297 11886.59 1.292875e-31 11892.57 2.024005e-31
## 80 TVMe+G(4)+I 67 -5878.736 11891.47 1.128095e-32 11897.64 1.609710e-32
## 40 TPM2+G(4)+I 65 -5881.346 11892.69 6.130644e-33 11898.49 1.051412e-32
## 70 TIM3e+I 65 -5883.586 11897.17 6.526699e-34 11902.97 1.119336e-33
## 18 TrNe+I 64 -5887.889 11903.78 2.399054e-35 11909.40 4.500685e-35
## 54 TIM1e+I 65 -5887.793 11905.59 9.720375e-36 11911.38 1.667055e-35
## 71 TIM3e+G(4) 65 -5888.332 11906.66 5.668745e-36 11912.46 9.721958e-36
## 79 TVMe+G(4) 66 -5887.499 11907.00 4.796991e-36 11912.98 7.509724e-36
## 39 TPM2+G(4) 64 -5889.941 11907.88 3.082044e-36 11913.50 5.781991e-36
## 19 TrNe+G(4) 64 -5890.955 11909.91 1.118053e-36 11915.53 2.097494e-36
## 55 TIM1e+G(4) 65 -5890.803 11911.61 4.789756e-37 11917.40 8.214482e-37
## 78 TVMe+I 66 -5896.951 11925.90 3.766415e-40 11931.88 5.896351e-40
## 38 TPM2+I 64 -5900.296 11928.59 9.816867e-41 11934.21 1.841668e-40
## 48 TPM3+G(4)+I 65 -5907.827 11945.65 1.935412e-44 11951.45 3.319252e-44
## 12 K80+G(4)+I 64 -5910.923 11949.85 2.381127e-45 11955.46 4.467054e-45
## 28 TPM1+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 32 K81+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 47 TPM3+G(4) 64 -5915.104 11958.21 3.637865e-47 11963.83 6.824725e-47
## 11 K80+G(4) 63 -5917.566 11961.13 8.427996e-48 11966.57 1.727014e-47
## 27 TPM1+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 31 K81+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 46 TPM3+I 64 -5922.373 11972.75 2.534994e-50 11978.36 4.755711e-50
## 10 K80+I 63 -5925.895 11977.79 2.036060e-51 11983.23 4.172171e-51
## 26 TPM1+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 30 K81+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 65 TIM2 67 -6222.408 12578.82 6.271235e-182 12584.98 8.948601e-182
## 89 GTR 69 -6222.154 12582.31 1.094453e-182 12588.85 1.291708e-182
## 41 TPM2u 66 -6234.278 12600.56 1.193748e-186 12606.54 1.868821e-186
## 61 TIM2e 64 -6237.587 12603.17 3.224702e-187 12608.79 6.049620e-187
## 81 TVM 68 -6233.969 12603.94 2.199107e-187 12610.29 2.855964e-187
## 85 SYM 66 -6237.480 12606.96 4.853013e-188 12612.94 7.597426e-188
## 8 F81+G(4)+I 66 -6263.407 12658.81 2.668370e-199 12664.79 4.177352e-199
## 21 TrN 66 -6263.725 12659.45 1.941635e-199 12665.43 3.039643e-199
## 73 TIM3 67 -6263.573 12661.15 8.311045e-200 12667.31 1.185926e-199
## 57 TIM1 67 -6263.631 12661.26 7.847574e-200 12667.43 1.119792e-199
## 6 F81+I 65 -6267.654 12665.31 1.037730e-200 12671.11 1.779718e-200
## 37 TPM2 63 -6275.356 12676.71 3.463739e-203 12682.15 7.097685e-203
## 77 TVMe 65 -6275.160 12680.32 5.706693e-204 12686.12 9.787040e-204
## 7 F81+G(4) 65 -6275.782 12681.56 3.061432e-204 12687.36 5.250389e-204
## 13 HKY 65 -6276.194 12682.39 2.027638e-204 12688.19 3.477420e-204
## 49 TPM3u 66 -6276.022 12684.04 8.867070e-205 12690.02 1.388146e-204
## 33 TPM1u 66 -6276.094 12684.19 8.243967e-205 12690.17 1.290599e-204
## 17 TrNe 63 -6296.975 12719.95 1.414288e-212 12725.39 2.898075e-212
## 69 TIM3e 64 -6296.937 12721.87 5.407528e-213 12727.49 1.014466e-212
## 53 TIM1e 64 -6296.938 12721.88 5.400399e-213 12727.49 1.013128e-212
## 9 K80 62 -6335.641 12795.28 6.202376e-229 12800.55 1.386198e-228
## 45 TPM3 63 -6335.582 12797.16 2.419369e-229 12802.61 4.957626e-229
## 25 TPM1 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 29 K81 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 4 JC+G(4)+I 63 -6340.357 12806.71 2.043113e-231 12812.15 4.186625e-231
## 2 JC+I 62 -6343.549 12811.10 2.280315e-232 12816.37 5.096384e-232
## 3 JC+G(4) 62 -6353.090 12830.18 1.639507e-236 12835.45 3.664211e-236
## 5 F81 64 -6638.961 13405.92 0.000000e+00 13411.54 0.000000e+00
## 1 JC 61 -6699.334 13520.67 0.000000e+00 13525.77 0.000000e+00
## BIC
## 92 12124.04
## 68 12116.98
## 84 12132.04
## 44 12124.08
## 90 12138.14
## 91 12141.91
## 76 12136.68
## 66 12132.20
## 67 12132.98
## 24 12136.27
## 60 12142.57
## 52 12139.86
## 83 12145.23
## 43 12135.88
## 82 12147.07
## 16 12138.82
## 36 12145.11
## 42 12140.47
## 75 12150.15
## 74 12150.36
## 23 12147.45
## 59 12154.21
## 51 12149.38
## 22 12150.74
## 15 12146.57
## 58 12157.30
## 50 12153.02
## 35 12153.38
## 14 12153.19
## 34 12159.65
## 88 12178.53
## 64 12172.34
## 86 12189.93
## 62 12184.43
## 87 12204.04
## 63 12195.71
## 72 12231.54
## 20 12232.41
## 56 12239.26
## 80 12249.48
## 40 12240.01
## 70 12244.49
## 18 12245.76
## 54 12252.91
## 71 12253.99
## 79 12259.66
## 39 12249.86
## 19 12251.89
## 55 12258.93
## 78 12278.57
## 38 12270.57
## 48 12292.98
## 12 12291.82
## 28 12298.52
## 32 12298.52
## 47 12300.19
## 11 12297.77
## 27 12304.83
## 31 12304.83
## 46 12314.73
## 10 12314.43
## 26 12321.38
## 30 12321.38
## 65 12936.83
## 89 12951.00
## 41 12953.22
## 61 12945.15
## 81 12967.29
## 85 12959.63
## 8 13011.48
## 21 13012.12
## 73 13019.16
## 57 13019.27
## 6 13012.63
## 37 13013.35
## 77 13027.64
## 7 13028.89
## 13 13029.71
## 49 13036.71
## 33 13036.85
## 17 13056.59
## 69 13063.85
## 53 13063.86
## 9 13126.57
## 45 13133.80
## 25 13133.84
## 29 13133.84
## 4 13143.35
## 2 13142.39
## 3 13161.47
## 5 13747.90
## 1 13846.62mySequences_modelTest[order(mySequences_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 68 TIM2+G(4)+I 69 -5805.140 11748.28 1.400575e-01 11754.82 1.653002e-01
## 92 GTR+G(4)+I 71 -5801.327 11744.65 8.585027e-01 11751.59 8.330917e-01
## 44 TPM2u+G(4)+I 68 -5812.364 11760.73 2.774303e-04 11767.08 3.602968e-04
## 84 TVM+G(4)+I 70 -5808.999 11758.00 1.086518e-03 11764.74 1.163642e-03
## 66 TIM2+I 68 -5816.425 11768.85 4.780728e-06 11775.20 6.208698e-06
## 67 TIM2+G(4) 68 -5816.814 11769.63 3.239588e-06 11775.98 4.207231e-06
## 43 TPM2u+G(4) 67 -5821.934 11777.87 5.260518e-08 11784.03 7.506381e-08
## 24 TrN+G(4)+I 68 -5818.456 11772.91 6.269809e-07 11779.27 8.142557e-07
## 76 TIM3+G(4)+I 69 -5814.993 11767.99 7.362056e-06 11774.53 8.688927e-06
## 90 GTR+I 70 -5812.051 11764.10 5.133160e-05 11770.84 5.497525e-05
## 16 HKY+G(4)+I 67 -5823.406 11780.81 1.208125e-08 11786.98 1.723908e-08
## 52 TPM3u+G(4)+I 68 -5820.253 11776.51 1.039606e-07 11782.86 1.350129e-07
## 42 TPM2u+I 67 -5824.232 11782.46 5.287646e-09 11788.63 7.545090e-09
## 91 GTR+G(4) 70 -5813.937 11767.87 7.784852e-06 11774.61 8.337440e-06
## 60 TIM1+G(4)+I 69 -5817.935 11773.87 3.886606e-07 11780.41 4.587093e-07
## 36 TPM1u+G(4)+I 68 -5822.876 11781.75 7.545176e-09 11788.11 9.798867e-09
## 83 TVM+G(4) 69 -5819.268 11776.54 1.024807e-07 11783.08 1.209509e-07
## 15 HKY+G(4) 66 -5830.950 11793.90 1.738266e-11 11799.88 2.721267e-11
## 82 TVM+I 69 -5820.188 11778.38 4.083387e-08 11784.92 4.819340e-08
## 23 TrN+G(4) 67 -5827.718 11789.44 1.619205e-10 11795.60 2.310489e-10
## 51 TPM3u+G(4) 67 -5828.685 11791.37 6.155710e-11 11797.54 8.783756e-11
## 75 TIM3+G(4) 68 -5825.397 11786.79 6.068114e-10 11793.15 7.880617e-10
## 74 TIM3+I 68 -5825.501 11787.00 5.465109e-10 11793.36 7.097499e-10
## 22 TrN+I 67 -5829.366 11792.73 3.114656e-11 11798.90 4.444390e-11
## 50 TPM3u+I 67 -5830.507 11795.01 9.954726e-12 11801.18 1.420468e-11
## 14 HKY+I 66 -5834.262 11800.52 6.333259e-13 11806.50 9.914763e-13
## 35 TPM1u+G(4) 67 -5830.683 11795.37 8.345047e-12 11801.53 1.190778e-11
## 59 TIM1+G(4) 68 -5827.429 11790.86 7.955656e-11 11797.21 1.033195e-10
## 58 TIM1+I 68 -5828.973 11793.95 1.698083e-11 11800.30 2.205289e-11
## 34 TPM1u+I 67 -5833.820 11801.64 3.622694e-13 11807.81 5.169324e-13
## 64 TIM2e+G(4)+I 66 -5843.839 11819.68 4.386452e-17 11825.66 6.867023e-17
## 88 SYM+G(4)+I 68 -5839.587 11815.17 4.172462e-16 11821.53 5.418747e-16
## 62 TIM2e+I 65 -5853.553 11837.11 7.205475e-21 11842.90 1.235747e-20
## 86 SYM+I 67 -5848.960 11831.92 9.635430e-20 11838.09 1.374907e-19
## 63 TIM2e+G(4) 65 -5859.192 11848.38 2.563529e-23 11854.18 4.396479e-23
## 87 SYM+G(4) 67 -5856.016 11846.03 8.311607e-23 11852.20 1.186007e-22
## 72 TIM3e+G(4)+I 66 -5873.437 11878.87 6.141221e-30 11884.85 9.614126e-30
## 20 TrNe+G(4)+I 65 -5877.541 11885.08 2.752968e-31 11890.88 4.721370e-31
## 56 TIM1e+G(4)+I 66 -5877.297 11886.59 1.292875e-31 11892.57 2.024005e-31
## 40 TPM2+G(4)+I 65 -5881.346 11892.69 6.130644e-33 11898.49 1.051412e-32
## 70 TIM3e+I 65 -5883.586 11897.17 6.526699e-34 11902.97 1.119336e-33
## 18 TrNe+I 64 -5887.889 11903.78 2.399054e-35 11909.40 4.500685e-35
## 80 TVMe+G(4)+I 67 -5878.736 11891.47 1.128095e-32 11897.64 1.609710e-32
## 39 TPM2+G(4) 64 -5889.941 11907.88 3.082044e-36 11913.50 5.781991e-36
## 19 TrNe+G(4) 64 -5890.955 11909.91 1.118053e-36 11915.53 2.097494e-36
## 54 TIM1e+I 65 -5887.793 11905.59 9.720375e-36 11911.38 1.667055e-35
## 71 TIM3e+G(4) 65 -5888.332 11906.66 5.668745e-36 11912.46 9.721958e-36
## 55 TIM1e+G(4) 65 -5890.803 11911.61 4.789756e-37 11917.40 8.214482e-37
## 79 TVMe+G(4) 66 -5887.499 11907.00 4.796991e-36 11912.98 7.509724e-36
## 38 TPM2+I 64 -5900.296 11928.59 9.816867e-41 11934.21 1.841668e-40
## 78 TVMe+I 66 -5896.951 11925.90 3.766415e-40 11931.88 5.896351e-40
## 12 K80+G(4)+I 64 -5910.923 11949.85 2.381127e-45 11955.46 4.467054e-45
## 48 TPM3+G(4)+I 65 -5907.827 11945.65 1.935412e-44 11951.45 3.319252e-44
## 11 K80+G(4) 63 -5917.566 11961.13 8.427996e-48 11966.57 1.727014e-47
## 28 TPM1+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 32 K81+G(4)+I 65 -5910.598 11951.20 1.211464e-45 11956.99 2.077674e-45
## 47 TPM3+G(4) 64 -5915.104 11958.21 3.637865e-47 11963.83 6.824725e-47
## 27 TPM1+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 31 K81+G(4) 64 -5917.427 11962.85 3.563659e-48 11968.47 6.685512e-48
## 10 K80+I 63 -5925.895 11977.79 2.036060e-51 11983.23 4.172171e-51
## 46 TPM3+I 64 -5922.373 11972.75 2.534994e-50 11978.36 4.755711e-50
## 26 TPM1+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 30 K81+I 64 -5925.700 11979.40 9.103314e-52 11985.02 1.707804e-51
## 65 TIM2 67 -6222.408 12578.82 6.271235e-182 12584.98 8.948601e-182
## 61 TIM2e 64 -6237.587 12603.17 3.224702e-187 12608.79 6.049620e-187
## 89 GTR 69 -6222.154 12582.31 1.094453e-182 12588.85 1.291708e-182
## 41 TPM2u 66 -6234.278 12600.56 1.193748e-186 12606.54 1.868821e-186
## 85 SYM 66 -6237.480 12606.96 4.853013e-188 12612.94 7.597426e-188
## 81 TVM 68 -6233.969 12603.94 2.199107e-187 12610.29 2.855964e-187
## 8 F81+G(4)+I 66 -6263.407 12658.81 2.668370e-199 12664.79 4.177352e-199
## 21 TrN 66 -6263.725 12659.45 1.941635e-199 12665.43 3.039643e-199
## 6 F81+I 65 -6267.654 12665.31 1.037730e-200 12671.11 1.779718e-200
## 37 TPM2 63 -6275.356 12676.71 3.463739e-203 12682.15 7.097685e-203
## 73 TIM3 67 -6263.573 12661.15 8.311045e-200 12667.31 1.185926e-199
## 57 TIM1 67 -6263.631 12661.26 7.847574e-200 12667.43 1.119792e-199
## 77 TVMe 65 -6275.160 12680.32 5.706693e-204 12686.12 9.787040e-204
## 7 F81+G(4) 65 -6275.782 12681.56 3.061432e-204 12687.36 5.250389e-204
## 13 HKY 65 -6276.194 12682.39 2.027638e-204 12688.19 3.477420e-204
## 49 TPM3u 66 -6276.022 12684.04 8.867070e-205 12690.02 1.388146e-204
## 33 TPM1u 66 -6276.094 12684.19 8.243967e-205 12690.17 1.290599e-204
## 17 TrNe 63 -6296.975 12719.95 1.414288e-212 12725.39 2.898075e-212
## 69 TIM3e 64 -6296.937 12721.87 5.407528e-213 12727.49 1.014466e-212
## 53 TIM1e 64 -6296.938 12721.88 5.400399e-213 12727.49 1.013128e-212
## 9 K80 62 -6335.641 12795.28 6.202376e-229 12800.55 1.386198e-228
## 45 TPM3 63 -6335.582 12797.16 2.419369e-229 12802.61 4.957626e-229
## 25 TPM1 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 29 K81 63 -6335.602 12797.20 2.373040e-229 12802.64 4.862691e-229
## 2 JC+I 62 -6343.549 12811.10 2.280315e-232 12816.37 5.096384e-232
## 4 JC+G(4)+I 63 -6340.357 12806.71 2.043113e-231 12812.15 4.186625e-231
## 3 JC+G(4) 62 -6353.090 12830.18 1.639507e-236 12835.45 3.664211e-236
## 5 F81 64 -6638.961 13405.92 0.000000e+00 13411.54 0.000000e+00
## 1 JC 61 -6699.334 13520.67 0.000000e+00 13525.77 0.000000e+00
## BIC
## 68 12116.98
## 92 12124.04
## 44 12124.08
## 84 12132.04
## 66 12132.20
## 67 12132.98
## 43 12135.88
## 24 12136.27
## 76 12136.68
## 90 12138.14
## 16 12138.82
## 52 12139.86
## 42 12140.47
## 91 12141.91
## 60 12142.57
## 36 12145.11
## 83 12145.23
## 15 12146.57
## 82 12147.07
## 23 12147.45
## 51 12149.38
## 75 12150.15
## 74 12150.36
## 22 12150.74
## 50 12153.02
## 14 12153.19
## 35 12153.38
## 59 12154.21
## 58 12157.30
## 34 12159.65
## 64 12172.34
## 88 12178.53
## 62 12184.43
## 86 12189.93
## 63 12195.71
## 87 12204.04
## 72 12231.54
## 20 12232.41
## 56 12239.26
## 40 12240.01
## 70 12244.49
## 18 12245.76
## 80 12249.48
## 39 12249.86
## 19 12251.89
## 54 12252.91
## 71 12253.99
## 55 12258.93
## 79 12259.66
## 38 12270.57
## 78 12278.57
## 12 12291.82
## 48 12292.98
## 11 12297.77
## 28 12298.52
## 32 12298.52
## 47 12300.19
## 27 12304.83
## 31 12304.83
## 10 12314.43
## 46 12314.73
## 26 12321.38
## 30 12321.38
## 65 12936.83
## 61 12945.15
## 89 12951.00
## 41 12953.22
## 85 12959.63
## 81 12967.29
## 8 13011.48
## 21 13012.12
## 6 13012.63
## 37 13013.35
## 73 13019.16
## 57 13019.27
## 77 13027.64
## 7 13028.89
## 13 13029.71
## 49 13036.71
## 33 13036.85
## 17 13056.59
## 69 13063.85
## 53 13063.86
## 9 13126.57
## 45 13133.80
## 25 13133.84
## 29 13133.84
## 2 13142.39
## 4 13143.35
## 3 13161.47
## 5 13747.90
## 1 13846.62Meilleur modele : TIM2+G(4)+I
env$`TIM2+G(4)+I`## pml(tree = `tree_TIM2+G(4)+I`, data = data, bf = c(0.268171757414785,
## 0.270827799911465, 0.170916334661355, 0.290084108012395), Q = c(7.62145716626704,
## 50.5284652228583, 7.62145716626704, 1, 86.6493750028368, 1),
## model = "TIM2", inv = 0.588100254543259, k = 4, shape = 2.68433431260428)v) Reconstruire l’arbre sélectionné à l’aide de modelTest() en utilisant les paramètres obtenus en iv.
#Matrice de distances par défaut (Jukes et Cantor)
dm <- dist.ml(mySequences_phangorn)
#Construction d'arbre par NJ
treeNJ <- NJ(dm)
#Calcul du score de maximum de vraisemblance
fit = pml(treeNJ, data=mySequences_phangorn)
#Phangorn nous permet de changer le modèle utilisé dans un objet
#On commence par intégrer les paramètres gamma et I (proportion de sites invariables)
fitTIM2 <- update(fit, k=4, inv=0.586110878594773, shape = 2.76728130721059)
#Recalcul des distances avec le modèle TIM2
fitTIM2 <- optim.pml(fitTIM2, model="TIM2", optInv=TRUE, optGamma=TRUE,optShape = TRUE, rearrangement = "stochastic", control = pml.control(trace = 0))
#Bootstrap
bs = bootstrap.pml(fitTIM2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE,control = pml.control(trace = 0))
#représentation graphique de l'arbre final
plotBS(midpoint(fitTIM2$tree), bs, p = 0, type="p", frame = "circle", cex = 0.6, bs.adj = c(0.5,0.5), bg = "white")
D) Reconstruction d’arbres et comparaison des cadres de lecture avec différents modèles d’AAs
i) Utiliser l’alignement traduit d’AAs avec la librairie phangorn et produire les matrices de distances avec les modèles évolutifs d’AAs suivants : LG, JTT et Blosum62.
Conversion
#Cadre de lecture par default (NA)
mySequences_align_aa_ape = as.AAbin(mySequences_align_aa)
mySequences_phangorn_aa = as.phyDat.AAbin(mySequences_align_aa_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.#Cadre de lecture choisie : 1
mySequences_align_aa__cadre_1_ape = as.AAbin(mySequences_align_aa_cadre_1)
mySequences_phangorn_aa_cadre_1 = as.phyDat.AAbin(mySequences_align_aa__cadre_1_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Matrice de distance
#Cadre de lecture par default (NA)
dist_LG <- dist.ml(mySequences_phangorn_aa, model = "LG")
dist_JTT <- dist.ml(mySequences_phangorn_aa, model = "JTT")
dist_Blosum62 <- dist.ml(mySequences_phangorn_aa, model = "Blosum62")
#Cadre de lecture choisie : 1
dist_LG_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "LG")
dist_JTT_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "JTT")
dist_Blosum62_cadre1 <- dist.ml(mySequences_phangorn_aa_cadre_1, model = "Blosum62")Graphique de la matrice de distance
plot(dist_LG, main = "Valeurs de distance entre les séquences pour LG pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_JTT, main = "Valeurs de distance entre les séquences pour JTT pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_Blosum62, main = "Valeurs de distance entre les séquences pour Blosum62 pour le cadre de lecture par defaut", ylab = "distance", xlab= "position")
plot(dist_LG_cadre1, main = "Valeurs de distance entre les séquences pour LG pour le cadre de lecture 1", ylab = "distance", xlab= "position")
plot(dist_JTT_cadre1, main = "Valeurs de distance entre les séquences pour JTT pour le cadre de lecture 1", ylab = "distance", xlab= "position")
plot(dist_Blosum62_cadre1, main = "Valeurs de distance entre les séquences pour Blosum62 pour le cadre de lecture 1", ylab = "distance", xlab= "position")
ii) Reconstruire les arbres en Neighbor-joining avec 1000 itérations de bootstrap et comparer les alignements avec le cadre de lecture choisi automatiquement, et le cadre de lecture modifié produit en b)ii.
Construction d’arbres avec le Neighbor-Joining
#Cadre de lecture par default (NA)
dist_LG_NJ <- NJ(dist_LG)
dist_JTT_NJ = NJ(dist_JTT)
dist_Blosum62_NJ = NJ(dist_Blosum62)
#Cadre de lecture choisie : 1
dist_LG_NJ_cadre1 = NJ(dist_LG_cadre1)
dist_JTT_NJ_cadre1 = NJ(dist_JTT_cadre1)
dist_Blosum62_NJ_cadre1 = NJ(dist_Blosum62_cadre1)Rechercher le meilleur modèle pour le cadre par defaut
mySequences_modelTest_aa = phangorn::modelTest(mySequences_phangorn_aa, model = c("JTT","LG", "Blosum62"))## Model df logLik AIC BIC
## JTT 61 -1790.436 3702.872 3961.171
## JTT+I 62 -1775.324 3674.647 3937.181
## JTT+G(4) 62 -1777.865 3679.731 3942.264
## JTT+G(4)+I 63 -1775.366 3676.731 3943.499
## LG 61 -1795.056 3712.113 3970.412
## LG+I 62 -1780.886 3685.771 3948.305
## LG+G(4) 62 -1782.945 3689.89 3952.424
## LG+G(4)+I 63 -1780.928 3687.856 3954.624
## Blosum62 61 -1789.301 3700.603 3958.902
## Blosum62+I 62 -1775.205 3674.411 3936.944
## Blosum62+G(4) 62 -1777.166 3678.332 3940.865
## Blosum62+G(4)+I 63 -1775.248 3676.496 3943.263mySequences_modelTest_aa[order(mySequences_modelTest_aa$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 10 Blosum62+I 62 -1775.205 3674.411 3.609940e-01 3691.887 3.851836e-01
## 2 JTT+I 62 -1775.324 3674.647 3.206953e-01 3692.124 3.421846e-01
## 12 Blosum62+G(4)+I 63 -1775.248 3676.496 1.272802e-01 3694.576 1.003984e-01
## 4 JTT+G(4)+I 63 -1775.366 3676.731 1.131422e-01 3694.812 8.924639e-02
## 11 Blosum62+G(4) 62 -1777.166 3678.332 5.081598e-02 3695.808 5.422108e-02
## 3 JTT+G(4) 62 -1777.865 3679.731 2.524804e-02 3697.207 2.693987e-02
## 6 LG+I 62 -1780.886 3685.771 1.231861e-03 3703.248 1.314406e-03
## 8 LG+G(4)+I 63 -1780.928 3687.856 4.343156e-04 3705.937 3.425873e-04
## 7 LG+G(4) 62 -1782.945 3689.890 1.570951e-04 3707.367 1.676218e-04
## 9 Blosum62 61 -1789.301 3700.603 7.411858e-07 3717.487 1.063585e-06
## 1 JTT 61 -1790.436 3702.872 2.383650e-07 3719.756 3.420486e-07
## 5 LG 61 -1795.056 3712.113 2.347661e-09 3728.996 3.368842e-09
## BIC
## 10 3936.944
## 2 3937.181
## 12 3943.263
## 4 3943.499
## 11 3940.865
## 3 3942.264
## 6 3948.305
## 8 3954.624
## 7 3952.424
## 9 3958.902
## 1 3961.171
## 5 3970.412mySequences_modelTest_aa[order(mySequences_modelTest_aa$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 10 Blosum62+I 62 -1775.205 3674.411 3.609940e-01 3691.887 3.851836e-01
## 2 JTT+I 62 -1775.324 3674.647 3.206953e-01 3692.124 3.421846e-01
## 11 Blosum62+G(4) 62 -1777.166 3678.332 5.081598e-02 3695.808 5.422108e-02
## 3 JTT+G(4) 62 -1777.865 3679.731 2.524804e-02 3697.207 2.693987e-02
## 12 Blosum62+G(4)+I 63 -1775.248 3676.496 1.272802e-01 3694.576 1.003984e-01
## 4 JTT+G(4)+I 63 -1775.366 3676.731 1.131422e-01 3694.812 8.924639e-02
## 6 LG+I 62 -1780.886 3685.771 1.231861e-03 3703.248 1.314406e-03
## 7 LG+G(4) 62 -1782.945 3689.890 1.570951e-04 3707.367 1.676218e-04
## 8 LG+G(4)+I 63 -1780.928 3687.856 4.343156e-04 3705.937 3.425873e-04
## 9 Blosum62 61 -1789.301 3700.603 7.411858e-07 3717.487 1.063585e-06
## 1 JTT 61 -1790.436 3702.872 2.383650e-07 3719.756 3.420486e-07
## 5 LG 61 -1795.056 3712.113 2.347661e-09 3728.996 3.368842e-09
## BIC
## 10 3936.944
## 2 3937.181
## 11 3940.865
## 3 3942.264
## 12 3943.263
## 4 3943.499
## 6 3948.305
## 7 3952.424
## 8 3954.624
## 9 3958.902
## 1 3961.171
## 5 3970.412Meilleur modele: Blosum62+I
Rechercher le meilleur modèle pour le cadre 1
mySequences_modelTest_aa_cadre_1 = phangorn::modelTest(mySequences_phangorn_aa_cadre_1, model = c("JTT","LG", "Blosum62"))## Model df logLik AIC BIC
## JTT 61 -2254.369 4630.738 4895.393
## JTT+I 62 -2251.546 4627.091 4896.084
## JTT+G(4) 62 -2250.274 4624.548 4893.54
## JTT+G(4)+I 63 -2250.274 4626.548 4899.879
## LG 61 -2254.105 4630.211 4894.865
## LG+I 62 -2251.311 4626.622 4895.615
## LG+G(4) 62 -2249.887 4623.775 4892.767
## LG+G(4)+I 63 -2249.856 4625.713 4899.044
## Blosum62 61 -2252.08 4626.16 4890.814
## Blosum62+I 62 -2251.753 4627.506 4896.499
## Blosum62+G(4) 62 -2250.298 4624.596 4893.589
## Blosum62+G(4)+I 63 -2250.283 4626.566 4899.898mySequences_modelTest_aa_cadre_1[order(mySequences_modelTest_aa_cadre_1$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 7 LG+G(4) 62 -2249.887 4623.775 0.239235093 4639.305 0.244698908
## 3 JTT+G(4) 62 -2250.274 4624.548 0.162556819 4640.078 0.166269403
## 11 Blosum62+G(4) 62 -2250.298 4624.596 0.158638275 4640.127 0.162261364
## 8 LG+G(4)+I 63 -2249.856 4625.713 0.090783704 4641.776 0.071136220
## 9 Blosum62 61 -2252.080 4626.160 0.072595937 4641.168 0.096440867
## 4 JTT+G(4)+I 63 -2250.274 4626.548 0.059787012 4642.612 0.046847857
## 12 Blosum62+G(4)+I 63 -2250.283 4626.566 0.059246558 4642.630 0.046424369
## 6 LG+I 62 -2251.311 4626.622 0.057620910 4642.153 0.058936896
## 2 JTT+I 62 -2251.546 4627.091 0.045568358 4642.622 0.046609080
## 10 Blosum62+I 62 -2251.753 4627.506 0.037034140 4643.037 0.037879951
## 5 LG 61 -2254.105 4630.211 0.009576460 4645.219 0.012721953
## 1 JTT 61 -2254.369 4630.738 0.007356733 4645.746 0.009773132
## BIC
## 7 4892.767
## 3 4893.540
## 11 4893.589
## 8 4899.044
## 9 4890.814
## 4 4899.879
## 12 4899.898
## 6 4895.615
## 2 4896.084
## 10 4896.499
## 5 4894.865
## 1 4895.393mySequences_modelTest_aa_cadre_1[order(mySequences_modelTest_aa_cadre_1$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 9 Blosum62 61 -2252.080 4626.160 0.072595937 4641.168 0.096440867
## 7 LG+G(4) 62 -2249.887 4623.775 0.239235093 4639.305 0.244698908
## 3 JTT+G(4) 62 -2250.274 4624.548 0.162556819 4640.078 0.166269403
## 11 Blosum62+G(4) 62 -2250.298 4624.596 0.158638275 4640.127 0.162261364
## 5 LG 61 -2254.105 4630.211 0.009576460 4645.219 0.012721953
## 1 JTT 61 -2254.369 4630.738 0.007356733 4645.746 0.009773132
## 6 LG+I 62 -2251.311 4626.622 0.057620910 4642.153 0.058936896
## 2 JTT+I 62 -2251.546 4627.091 0.045568358 4642.622 0.046609080
## 10 Blosum62+I 62 -2251.753 4627.506 0.037034140 4643.037 0.037879951
## 8 LG+G(4)+I 63 -2249.856 4625.713 0.090783704 4641.776 0.071136220
## 4 JTT+G(4)+I 63 -2250.274 4626.548 0.059787012 4642.612 0.046847857
## 12 Blosum62+G(4)+I 63 -2250.283 4626.566 0.059246558 4642.630 0.046424369
## BIC
## 9 4890.814
## 7 4892.767
## 3 4893.540
## 11 4893.589
## 5 4894.865
## 1 4895.393
## 6 4895.615
## 2 4896.084
## 10 4896.499
## 8 4899.044
## 4 4899.879
## 12 4899.898Meilleur modele cadre 1 : LG+G(4)
Bootstrap avec 1000 iterations
#Cadre de lecture par default (NA)
dist_LG_NJ_boot <- bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "LG")), bs = 1000)
dist_JTT_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "JTT")), bs = 1000)
dist_Blosum62_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa, FUN = function(x) NJ(dist.ml(x, model = "Blosum62")), bs = 1000)
#Cadre de lecture choisie : 1
dist_cadre_1_LG_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "LG")), bs = 1000)
dist_cadre_1_JTT_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "JTT")), bs = 1000)
dist_cadre_1_Blosum62_NJ_boot = bootstrap.phyDat(mySequences_phangorn_aa_cadre_1, FUN = function(x) NJ(dist.ml(x, model = "Blosum62")), bs = 1000)Générer un arbre consensuel à partir de l’ensemble d’arbres issus des itérations de bootstrap
p = 0.5 : une branche doit être “supportée” par au moins 50% des itérations pour être considérée dans l’arbre consensuel final.
#Cadre de lecture par default (NA)
cons_LG <- consensus(dist_LG_NJ_boot, p = 0.5)
cons_JTT <- consensus(dist_JTT_NJ_boot, p = 0.5)
cons_Blosum62 <- consensus(dist_Blosum62_NJ_boot, p = 0.5)
#Cadre de lecture choisie : 1
cons_cadre_1_LG <- consensus(dist_cadre_1_LG_NJ_boot, p = 0.5)
cons_cadre_1_JTT <- consensus(dist_cadre_1_JTT_NJ_boot, p = 0.5)
cons_cadre_1_Blosum62 <- consensus(dist_cadre_1_Blosum62_NJ_boot, p = 0.5)Comparaison des bootstraps
bootstrap_comparisons <- round(cor(cbind(cons_LG$node.label,cons_JTT$node.label,cons_Blosum62$node.label, cons_cadre_1_LG$node.label,cons_cadre_1_JTT$node.label,cons_cadre_1_Blosum62$node.label )),3)## Warning in cbind(...): number of rows of result is not a multiple of vector
## length (arg 5)# Ajouter les noms aux colonnes et aux lignes
colnames(bootstrap_comparisons) <- c("LG", "JTT", "Blosum62", "LG_cadre1", "JTT_cadre1", "Blosum62_cadre1")
rownames(bootstrap_comparisons) <- c("LG", "JTT", "Blosum62", "LG_cadre1", "JTT_cadre1", "Blosum62_cadre1")
bootstrap_comparisons## LG JTT Blosum62 LG_cadre1 JTT_cadre1 Blosum62_cadre1
## LG 1.000 0.986 0.978 0.599 0.337 0.177
## JTT 0.986 1.000 0.982 0.594 0.362 0.158
## Blosum62 0.978 0.982 1.000 0.473 0.269 0.197
## LG_cadre1 0.599 0.594 0.473 1.000 0.363 -0.009
## JTT_cadre1 0.337 0.362 0.269 0.363 1.000 0.048
## Blosum62_cadre1 0.177 0.158 0.197 -0.009 0.048 1.000Visualisation des bootstraps
plot(cons_LG, main = "LG, cadre par defaut", no.margin = TRUE)
nodelabels(cons_LG$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_JTT,, main = "JTT, cadre par defaut", no.margin = TRUE)
nodelabels(cons_JTT$node.label * 100, bg = "white", frame = "circle", cex = 0.6)
plot(cons_Blosum62, main = "Blosum62, cadre par defaut", no.margin = TRUE)
nodelabels(cons_Blosum62$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_LG, main = "LG, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_LG$node.label * 100,
bg ="white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_JTT, main = "JTT, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_JTT$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
plot(cons_cadre_1_Blosum62,main = "Blosum62, cadre 1", no.margin = TRUE)
nodelabels(cons_cadre_1_Blosum62$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
E) Pour le jeu de données du gène codant « COI » des Cétacés, faire des alignements pour chaque cadre de lecture possible.
Alignements
# Cadre 1
Align_aa_cadre1 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 1,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.06 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.06 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs# Cadre 2
Align_aa_cadre2 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 2,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 0.03 secs# Cadre 3
Align_aa_cadre3 = AlignTranslation(mySequences,
sense = "+",
readingFrame = 3,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.1 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.07 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 0.02 secsConversions
# Cadre 1
Align_aa_cadre1_ape = as.AAbin(Align_aa_cadre1)
Align_aa_cadre1_phangorn = as.phyDat.AAbin(Align_aa_cadre1_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.# Cadre 2
Align_aa_cadre2_ape = as.AAbin(Align_aa_cadre2)
Align_aa_cadre2_phangorn = as.phyDat.AAbin(Align_aa_cadre2_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.# Cadre 3
Align_aa_cadre3_ape = as.AAbin(Align_aa_cadre3)
Align_aa_cadre3_phangorn = as.phyDat.AAbin(Align_aa_cadre3_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.i) Utiliser la fonction modelTest() pour trouver le meilleur modèle pour chaque cadre de lecture.
# Cadre 1
modelTest_aa_cadre1 = phangorn::modelTest(Align_aa_cadre1_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 61 -2263.381 4648.762 4913.416
## WAG+I 62 -2261.887 4647.774 4916.767
## WAG+G(4) 62 -2260.337 4644.675 4913.668
## WAG+G(4)+I 63 -2260.298 4646.597 4919.928
## JTT 61 -2260.149 4642.297 4906.951
## JTT+I 62 -2257.322 4638.645 4907.637
## JTT+G(4) 62 -2255.785 4635.57 4904.563
## JTT+G(4)+I 63 -2255.785 4637.571 4910.902
## LG 61 -2259.409 4640.818 4905.472
## LG+I 62 -2256.612 4637.223 4906.216
## LG+G(4) 62 -2254.886 4633.773 4902.766
## LG+G(4)+I 63 -2254.857 4635.714 4909.045
## Dayhoff 61 -2344.747 4811.493 5076.147
## Dayhoff+I 62 -2286.289 4696.578 4965.571
## Dayhoff+G(4) 62 -2347.623 4819.246 5088.239
## Dayhoff+G(4)+I 63 -2351.927 4829.853 5103.185
## cpREV 61 -2244.43 4610.86 4875.514
## cpREV+I 62 -2243.668 4611.336 4880.328
## cpREV+G(4) 62 -2241.094 4606.189 4875.181
## cpREV+G(4)+I 63 -2241.053 4608.105 4881.437
## mtmam 61 -2305.294 4732.587 4997.242
## mtmam+I 62 -2302.664 4729.329 4998.321
## mtmam+G(4) 62 -2304.277 4732.554 5001.547
## mtmam+G(4)+I 63 -2302.695 4731.389 5004.721
## mtArt 61 -2197.083 4516.167 4780.821
## mtArt+I 62 -2194.926 4513.851 4782.844
## mtArt+G(4) 62 -2192.365 4508.731 4777.724
## mtArt+G(4)+I 63 -2192.204 4510.408 4783.739
## MtZoa 61 -2184.753 4491.506 4756.161
## MtZoa+I 62 -2183.359 4490.717 4759.71
## MtZoa+G(4) 62 -2181.142 4486.283 4755.276
## MtZoa+G(4)+I 63 -2181.117 4488.233 4761.565
## mtREV24 61 -2200.49 4522.979 4787.634
## mtREV24+I 62 -2198.709 4521.418 4790.41
## mtREV24+G(4) 62 -2194.307 4512.613 4781.606
## mtREV24+G(4)+I 63 -2194.307 4514.613 4787.945
## VT 61 -2254.936 4631.871 4896.525
## VT+I 62 -2253.329 4630.659 4899.651
## VT+G(4) 62 -2249.596 4623.192 4892.184
## VT+G(4)+I 63 -2249.596 4625.192 4898.524
## RtREV 61 -2270.525 4663.05 4927.704
## RtREV+I 62 -2268.845 4661.69 4930.683
## RtREV+G(4) 62 -2266.996 4657.991 4926.984
## RtREV+G(4)+I 63 -2266.991 4659.982 4933.314
## HIVw 61 -2352.958 4827.917 5092.571
## HIVw+I 62 -2343.931 4811.862 5080.855
## HIVw+G(4) 62 -2339.832 4803.664 5072.657
## HIVw+G(4)+I 63 -2339.787 4805.574 5078.906
## HIVb 61 -2288.961 4699.921 4964.575
## HIVb+I 62 -2284.819 4693.638 4962.631
## HIVb+G(4) 62 -2283.384 4690.768 4959.761
## HIVb+G(4)+I 63 -2283.457 4692.914 4966.246
## FLU 61 -2288.97 4699.94 4964.594
## FLU+I 62 -2285.155 4694.311 4963.304
## FLU+G(4) 62 -2285.704 4695.408 4964.401
## FLU+G(4)+I 63 -2284.923 4695.846 4969.177
## Blosum62 61 -2257.9 4637.8 4902.454
## Blosum62+I 62 -2257.572 4639.144 4908.136
## Blosum62+G(4) 62 -2255.824 4635.648 4904.641
## Blosum62+G(4)+I 63 -2255.807 4637.614 4910.946
## Dayhoff_DCMut 61 -2344.547 4811.094 5075.748
## Dayhoff_DCMut+I 62 -2347.441 4818.882 5087.875
## Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 5087.837
## Dayhoff_DCMut+G(4)+I 63 -2347.55 4821.101 5094.432
## JTT_DCMut 61 -2260.683 4643.365 4908.02
## JTT_DCMut+I 62 -2257.895 4639.791 4908.784
## JTT_DCMut+G(4) 62 -2256.351 4636.702 4905.695
## JTT_DCMut+G(4)+I 63 -2256.351 4638.702 4912.034# Cadre 2
modelTest_aa_cadre2 = phangorn::modelTest(Align_aa_cadre2_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 61 -5573.273 11268.55 11532.44
## WAG+I 62 -5571.499 11267 11535.22
## WAG+G(4) 62 -5565.296 11254.59 11522.81
## WAG+G(4)+I 63 -5565.296 11256.59 11529.14
## JTT 61 -5272.829 10667.66 10931.55
## JTT+I 62 -5271.67 10667.34 10935.56
## JTT+G(4) 62 -5270.491 10664.98 10933.2
## JTT+G(4)+I 63 -5270.338 10666.68 10939.22
## LG 61 -5734.226 11590.45 11854.35
## LG+I 62 -5732.276 11588.55 11856.77
## LG+G(4) 62 -5722.814 11569.63 11837.85
## LG+G(4)+I 63 -5722.815 11571.63 11844.18
## Dayhoff 61 -5666.569 11455.14 11719.03
## Dayhoff+I 62 -5661.948 11447.9 11716.12
## Dayhoff+G(4) 62 -5654.7 11433.4 11701.62
## Dayhoff+G(4)+I 63 -5654.509 11435.02 11707.57
## cpREV 61 -5518.954 11159.91 11423.8
## cpREV+I 62 -5515.34 11154.68 11422.9
## cpREV+G(4) 62 -5505.296 11134.59 11402.81
## cpREV+G(4)+I 63 -5505.264 11136.53 11409.07
## mtmam 61 -5520.483 11162.97 11426.86
## mtmam+I 62 -5520.063 11164.13 11432.35
## mtmam+G(4) 62 -5504.986 11133.97 11402.19
## mtmam+G(4)+I 63 -5504.987 11135.97 11408.52
## mtArt 61 -5988.27 12098.54 12362.44
## mtArt+I 62 -5976.513 12077.03 12345.25
## mtArt+G(4) 62 -5878.724 11881.45 12149.67
## mtArt+G(4)+I 63 -5878.727 11883.45 12156
## MtZoa 61 -5839.378 11800.76 12064.65
## MtZoa+I 62 -5832.736 11789.47 12057.69
## MtZoa+G(4) 62 -5780.309 11684.62 11952.84
## MtZoa+G(4)+I 63 -5780.31 11686.62 11959.17
## mtREV24 61 -5477.613 11077.23 11341.12
## mtREV24+I 62 -5476.042 11076.08 11344.31
## mtREV24+G(4) 62 -5453.626 11031.25 11299.47
## mtREV24+G(4)+I 63 -5453.627 11033.25 11305.8
## VT 61 -5715.503 11553.01 11816.9
## VT+I 62 -5713.168 11550.34 11818.56
## VT+G(4) 62 -5701.884 11527.77 11795.99
## VT+G(4)+I 63 -5701.862 11529.72 11802.27
## RtREV 61 -5773.701 11669.4 11933.3
## RtREV+I 62 -5770.184 11664.37 11932.59
## RtREV+G(4) 62 -5757.388 11638.78 11907
## RtREV+G(4)+I 63 -5757.38 11640.76 11913.31
## HIVw 61 -5105.614 10333.23 10597.12
## HIVw+I 62 -5101.986 10327.97 10596.19
## HIVw+G(4) 62 -5102.354 10328.71 10596.93
## HIVw+G(4)+I 63 -5100.988 10327.98 10600.52
## HIVb 61 -5237.43 10596.86 10860.75
## HIVb+I 62 -5235.771 10595.54 10863.76
## HIVb+G(4) 62 -5231.911 10587.82 10856.04
## HIVb+G(4)+I 63 -5231.855 10589.71 10862.26
## FLU 61 -5329.737 10781.47 11045.37
## FLU+I 62 -5328.047 10780.09 11048.31
## FLU+G(4) 62 -5323.252 10770.5 11038.72
## FLU+G(4)+I 63 -5323.22 10772.44 11044.99
## Blosum62 61 -5725.452 11572.9 11836.8
## Blosum62+I 62 -5724.758 11573.52 11841.74
## Blosum62+G(4) 62 -5717.55 11559.1 11827.32
## Blosum62+G(4)+I 63 -5717.552 11561.1 11833.65
## Dayhoff_DCMut 61 -5666.022 11454.04 11717.94
## Dayhoff_DCMut+I 62 -5661.455 11446.91 11715.13
## Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 11700.88
## Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 11706.82
## JTT_DCMut 61 -5272.287 10666.57 10930.47
## JTT_DCMut+I 62 -5271.007 10666.01 10934.23
## JTT_DCMut+G(4) 62 -5269.726 10663.45 10931.67
## JTT_DCMut+G(4)+I 63 -5269.558 10665.12 10937.66# Cadre 3
modelTest_aa_cadre3 = phangorn::modelTest(Align_aa_cadre3_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 61 -5555.198 11232.4 11493.39
## WAG+I 62 -5551.78 11227.56 11492.83
## WAG+G(4) 62 -5541.009 11206.02 11471.29
## WAG+G(4)+I 63 -5541.007 11208.01 11477.56
## JTT 61 -5360.294 10842.59 11103.58
## JTT+I 62 -5357.455 10838.91 11104.18
## JTT+G(4) 62 -5348.833 10821.67 11086.93
## JTT+G(4)+I 63 -5348.822 10823.64 11093.19
## LG 61 -5614.854 11351.71 11612.7
## LG+I 62 -5610.756 11345.51 11610.78
## LG+G(4) 62 -5596.215 11316.43 11581.7
## LG+G(4)+I 63 -5596.215 11318.43 11587.98
## Dayhoff 61 -5642.067 11406.13 11667.12
## Dayhoff+I 62 -5638.096 11400.19 11665.46
## Dayhoff+G(4) 62 -5620.341 11364.68 11629.95
## Dayhoff+G(4)+I 63 -5620.411 11366.82 11636.37
## cpREV 61 -5477.362 11076.72 11337.71
## cpREV+I 62 -5470.87 11065.74 11331.01
## cpREV+G(4) 62 -5448.791 11021.58 11286.85
## cpREV+G(4)+I 63 -5448.787 11023.57 11293.12
## mtmam 61 -5378.721 10879.44 11140.43
## mtmam+I 62 -5377.876 10879.75 11145.02
## mtmam+G(4) 62 -5348.536 10821.07 11086.34
## mtmam+G(4)+I 63 -5348.536 10823.07 11092.62
## mtArt 61 -5837.166 11796.33 12057.32
## mtArt+I 62 -5825.196 11774.39 12039.66
## mtArt+G(4) 62 -5735.987 11595.97 11861.24
## mtArt+G(4)+I 63 -5735.988 11597.98 11867.52
## MtZoa 61 -5631.963 11385.93 11646.92
## MtZoa+I 62 -5623.709 11371.42 11636.69
## MtZoa+G(4) 62 -5563.323 11250.65 11515.91
## MtZoa+G(4)+I 63 -5563.324 11252.65 11522.2
## mtREV24 61 -5482.664 11087.33 11348.32
## mtREV24+I 62 -5475.823 11075.65 11340.91
## mtREV24+G(4) 62 -5437.664 10999.33 11264.6
## mtREV24+G(4)+I 63 -5437.664 11001.33 11270.88
## VT 61 -5856.713 11835.43 12096.42
## VT+I 62 -5844.255 11812.51 12077.78
## VT+G(4) 62 -5802.941 11729.88 11995.15
## VT+G(4)+I 63 -5802.941 11731.88 12001.43
## RtREV 61 -5758.647 11639.29 11900.28
## RtREV+I 62 -5754.169 11632.34 11897.61
## RtREV+G(4) 62 -5739.59 11603.18 11868.45
## RtREV+G(4)+I 63 -5739.561 11605.12 11874.67
## HIVw 61 -5296.14 10714.28 10975.27
## HIVw+I 62 -5289.262 10702.52 10967.79
## HIVw+G(4) 62 -5274.747 10673.49 10938.76
## HIVw+G(4)+I 63 -5274.432 10674.86 10944.41
## HIVb 61 -5408.02 10938.04 11199.03
## HIVb+I 62 -5403.549 10931.1 11196.37
## HIVb+G(4) 62 -5386.722 10897.44 11162.71
## HIVb+G(4)+I 63 -5386.72 10899.44 11168.99
## FLU 61 -5404.973 10931.95 11192.93
## FLU+I 62 -5398.516 10921.03 11186.3
## FLU+G(4) 62 -5372.332 10868.66 11133.93
## FLU+G(4)+I 63 -5372.299 10870.6 11140.14
## Blosum62 61 -5729.07 11580.14 11841.13
## Blosum62+I 62 -5725.072 11574.14 11839.41
## Blosum62+G(4) 62 -5715.334 11554.67 11819.94
## Blosum62+G(4)+I 63 -5715.306 11556.61 11826.16
## Dayhoff_DCMut 61 -5641.668 11405.34 11666.33
## Dayhoff_DCMut+I 62 -5637.732 11399.46 11664.73
## Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 11629.6
## Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 11636.02
## JTT_DCMut 61 -5369.642 10861.28 11122.27
## JTT_DCMut+I 62 -5366.753 10857.51 11122.77
## JTT_DCMut+G(4) 62 -5357.833 10839.67 11104.93
## JTT_DCMut+G(4)+I 63 -5357.824 10841.65 11111.19Trouver le meilleur modele
# Cadre 1
env <- attr(modelTest_aa_cadre1, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"modelTest_aa_cadre1[order(modelTest_aa_cadre1$AIC), ]## Model df logLik AIC AICw AICc
## 31 MtZoa+G(4) 62 -2181.142 4486.283 6.412018e-01 4501.814
## 32 MtZoa+G(4)+I 63 -2181.117 4488.233 2.418431e-01 4504.297
## 30 MtZoa+I 62 -2183.359 4490.717 6.985883e-02 4506.248
## 29 MtZoa 61 -2184.753 4491.506 4.708150e-02 4506.514
## 27 mtArt+G(4) 62 -2192.365 4508.731 8.563006e-06 4524.261
## 28 mtArt+G(4)+I 63 -2192.204 4510.408 3.701626e-06 4526.472
## 35 mtREV24+G(4) 62 -2194.307 4512.613 1.229028e-06 4528.144
## 26 mtArt+I 62 -2194.926 4513.851 6.617641e-07 4529.382
## 36 mtREV24+G(4)+I 63 -2194.307 4514.613 4.520787e-07 4530.677
## 25 mtArt 61 -2197.083 4516.167 2.079078e-07 4531.175
## 34 mtREV24+I 62 -2198.709 4521.418 1.505530e-08 4536.948
## 33 mtREV24 61 -2200.490 4522.979 6.895727e-09 4537.987
## 19 cpREV+G(4) 62 -2241.094 4606.189 5.887188e-27 4621.719
## 20 cpREV+G(4)+I 63 -2241.053 4608.105 2.257869e-27 4624.169
## 17 cpREV 61 -2244.430 4610.860 5.696190e-28 4625.868
## 18 cpREV+I 62 -2243.668 4611.336 4.489985e-28 4626.866
## 39 VT+G(4) 62 -2249.596 4623.192 1.196018e-30 4638.722
## 40 VT+G(4)+I 63 -2249.596 4625.192 4.398502e-31 4641.256
## 38 VT+I 62 -2253.329 4630.659 2.859660e-32 4646.189
## 37 VT 61 -2254.936 4631.871 1.559521e-32 4646.879
## 11 LG+G(4) 62 -2254.886 4633.773 6.026988e-33 4649.303
## 7 JTT+G(4) 62 -2255.785 4635.570 2.453398e-33 4651.101
## 59 Blosum62+G(4) 62 -2255.824 4635.648 2.360112e-33 4651.179
## 12 LG+G(4)+I 63 -2254.857 4635.714 2.283664e-33 4651.777
## 67 JTT_DCMut+G(4) 62 -2256.351 4636.702 1.393216e-33 4652.233
## 10 LG+I 62 -2256.612 4637.223 1.073514e-33 4652.754
## 8 JTT+G(4)+I 63 -2255.785 4637.571 9.023447e-34 4653.634
## 60 Blosum62+G(4)+I 63 -2255.807 4637.614 8.828675e-34 4653.678
## 57 Blosum62 61 -2257.900 4637.800 8.045825e-34 4652.808
## 6 JTT+I 62 -2257.322 4638.645 5.274485e-34 4654.175
## 68 JTT_DCMut+G(4)+I 63 -2256.351 4638.702 5.124147e-34 4654.766
## 58 Blosum62+I 62 -2257.572 4639.144 4.109857e-34 4654.674
## 66 JTT_DCMut+I 62 -2257.895 4639.791 2.973330e-34 4655.322
## 9 LG 61 -2259.409 4640.818 1.779159e-34 4655.826
## 5 JTT 61 -2260.149 4642.297 8.492553e-35 4657.305
## 65 JTT_DCMut 61 -2260.683 4643.365 4.978408e-35 4658.373
## 3 WAG+G(4) 62 -2260.337 4644.675 2.586405e-35 4660.206
## 4 WAG+G(4)+I 63 -2260.298 4646.597 9.894474e-36 4662.660
## 2 WAG+I 62 -2261.887 4647.774 5.491625e-36 4663.305
## 1 WAG 61 -2263.381 4648.762 3.351107e-36 4663.770
## 43 RtREV+G(4) 62 -2266.996 4657.991 3.319483e-38 4673.522
## 44 RtREV+G(4)+I 63 -2266.991 4659.982 1.226873e-38 4676.046
## 42 RtREV+I 62 -2268.845 4661.690 5.223955e-39 4677.220
## 41 RtREV 61 -2270.525 4663.050 2.646470e-39 4678.058
## 51 HIVb+G(4) 62 -2283.384 4690.768 2.533149e-45 4706.299
## 52 HIVb+G(4)+I 63 -2283.457 4692.914 8.662389e-46 4708.978
## 50 HIVb+I 62 -2284.819 4693.638 6.031978e-46 4709.169
## 54 FLU+I 62 -2285.155 4694.311 4.309048e-46 4709.842
## 55 FLU+G(4) 62 -2285.704 4695.408 2.489500e-46 4710.939
## 56 FLU+G(4)+I 63 -2284.923 4695.846 2.000513e-46 4711.909
## 14 Dayhoff+I 62 -2286.289 4696.578 1.387176e-46 4712.109
## 49 HIVb 61 -2288.961 4699.921 2.607059e-47 4714.929
## 53 FLU 61 -2288.970 4699.940 2.582352e-47 4714.948
## 22 mtmam+I 62 -2302.664 4729.329 1.072519e-53 4744.859
## 24 mtmam+G(4)+I 63 -2302.695 4731.389 3.827892e-54 4747.453
## 23 mtmam+G(4) 62 -2304.277 4732.554 2.137519e-54 4748.085
## 21 mtmam 61 -2305.294 4732.587 2.102600e-54 4747.595
## 47 HIVw+G(4) 62 -2339.832 4803.664 7.738658e-70 4819.195
## 48 HIVw+G(4)+I 63 -2339.787 4805.574 2.977609e-70 4821.638
## 61 Dayhoff_DCMut 61 -2344.547 4811.094 1.884843e-71 4826.102
## 13 Dayhoff 61 -2344.747 4811.493 1.543860e-71 4826.501
## 46 HIVw+I 62 -2343.931 4811.862 1.283894e-71 4827.393
## 63 Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 3.910641e-73 4834.375
## 62 Dayhoff_DCMut+I 62 -2347.441 4818.882 3.838174e-73 4834.413
## 15 Dayhoff+G(4) 62 -2347.623 4819.246 3.199604e-73 4834.777
## 64 Dayhoff_DCMut+G(4)+I 63 -2347.550 4821.101 1.265703e-73 4837.164
## 45 HIVw 61 -2352.958 4827.917 4.190232e-75 4842.925
## 16 Dayhoff+G(4)+I 63 -2351.927 4829.853 1.591242e-75 4845.917
## AICcw BIC
## 31 6.696654e-01 4755.276
## 32 1.934962e-01 4761.565
## 30 7.295994e-02 4759.710
## 29 6.386385e-02 4756.161
## 27 8.943127e-06 4777.724
## 28 2.961634e-06 4783.739
## 35 1.283586e-06 4781.606
## 26 6.911406e-07 4782.844
## 36 3.617037e-07 4787.945
## 25 2.820172e-07 4780.821
## 34 1.572362e-08 4790.410
## 33 9.353731e-09 4787.634
## 19 6.148527e-27 4875.181
## 20 1.806498e-27 4881.437
## 17 7.726615e-28 4875.514
## 18 4.689300e-28 4880.328
## 39 1.249111e-30 4892.184
## 40 3.519198e-31 4898.524
## 38 2.986603e-32 4899.651
## 37 2.115418e-32 4896.525
## 11 6.294533e-33 4902.766
## 7 2.562307e-33 4904.563
## 59 2.464880e-33 4904.641
## 12 1.827137e-33 4909.045
## 67 1.455063e-33 4905.695
## 10 1.121168e-33 4906.216
## 8 7.219571e-34 4910.902
## 60 7.063736e-34 4910.946
## 57 1.091378e-33 4902.454
## 6 5.508625e-34 4907.637
## 68 4.099779e-34 4912.034
## 58 4.292298e-34 4908.136
## 66 3.105320e-34 4908.784
## 9 2.413346e-34 4905.472
## 5 1.151975e-34 4906.951
## 65 6.752978e-35 4908.020
## 3 2.701218e-35 4913.668
## 4 7.916471e-36 4919.928
## 2 5.735404e-36 4916.767
## 1 4.545620e-36 4913.416
## 43 3.466838e-38 4926.984
## 44 9.816090e-39 4933.314
## 42 5.455852e-39 4930.683
## 41 3.589813e-39 4927.704
## 51 2.645598e-45 4959.761
## 52 6.930691e-46 4966.246
## 50 6.299744e-46 4962.631
## 54 4.500331e-46 4963.304
## 55 2.600012e-46 4964.401
## 56 1.600591e-46 4969.177
## 14 1.448754e-46 4965.571
## 49 3.536354e-47 4964.575
## 53 3.502839e-47 4964.594
## 22 1.120130e-53 4998.321
## 24 3.062659e-54 5004.721
## 23 2.232406e-54 5001.547
## 21 2.852079e-54 4997.242
## 47 8.082185e-70 5072.657
## 48 2.382355e-70 5078.906
## 61 2.556701e-71 5075.748
## 13 2.094174e-71 5076.147
## 46 1.340888e-71 5080.855
## 63 4.084238e-73 5087.837
## 62 4.008554e-73 5087.875
## 15 3.341638e-73 5088.239
## 64 1.012676e-73 5094.432
## 45 5.683853e-75 5092.571
## 16 1.273137e-75 5103.185modelTest_aa_cadre1[order(modelTest_aa_cadre1$BIC), ]## Model df logLik AIC AICw AICc
## 31 MtZoa+G(4) 62 -2181.142 4486.283 6.412018e-01 4501.814
## 29 MtZoa 61 -2184.753 4491.506 4.708150e-02 4506.514
## 30 MtZoa+I 62 -2183.359 4490.717 6.985883e-02 4506.248
## 32 MtZoa+G(4)+I 63 -2181.117 4488.233 2.418431e-01 4504.297
## 27 mtArt+G(4) 62 -2192.365 4508.731 8.563006e-06 4524.261
## 25 mtArt 61 -2197.083 4516.167 2.079078e-07 4531.175
## 35 mtREV24+G(4) 62 -2194.307 4512.613 1.229028e-06 4528.144
## 26 mtArt+I 62 -2194.926 4513.851 6.617641e-07 4529.382
## 28 mtArt+G(4)+I 63 -2192.204 4510.408 3.701626e-06 4526.472
## 33 mtREV24 61 -2200.490 4522.979 6.895727e-09 4537.987
## 36 mtREV24+G(4)+I 63 -2194.307 4514.613 4.520787e-07 4530.677
## 34 mtREV24+I 62 -2198.709 4521.418 1.505530e-08 4536.948
## 19 cpREV+G(4) 62 -2241.094 4606.189 5.887188e-27 4621.719
## 17 cpREV 61 -2244.430 4610.860 5.696190e-28 4625.868
## 18 cpREV+I 62 -2243.668 4611.336 4.489985e-28 4626.866
## 20 cpREV+G(4)+I 63 -2241.053 4608.105 2.257869e-27 4624.169
## 39 VT+G(4) 62 -2249.596 4623.192 1.196018e-30 4638.722
## 37 VT 61 -2254.936 4631.871 1.559521e-32 4646.879
## 40 VT+G(4)+I 63 -2249.596 4625.192 4.398502e-31 4641.256
## 38 VT+I 62 -2253.329 4630.659 2.859660e-32 4646.189
## 57 Blosum62 61 -2257.900 4637.800 8.045825e-34 4652.808
## 11 LG+G(4) 62 -2254.886 4633.773 6.026988e-33 4649.303
## 7 JTT+G(4) 62 -2255.785 4635.570 2.453398e-33 4651.101
## 59 Blosum62+G(4) 62 -2255.824 4635.648 2.360112e-33 4651.179
## 9 LG 61 -2259.409 4640.818 1.779159e-34 4655.826
## 67 JTT_DCMut+G(4) 62 -2256.351 4636.702 1.393216e-33 4652.233
## 10 LG+I 62 -2256.612 4637.223 1.073514e-33 4652.754
## 5 JTT 61 -2260.149 4642.297 8.492553e-35 4657.305
## 6 JTT+I 62 -2257.322 4638.645 5.274485e-34 4654.175
## 65 JTT_DCMut 61 -2260.683 4643.365 4.978408e-35 4658.373
## 58 Blosum62+I 62 -2257.572 4639.144 4.109857e-34 4654.674
## 66 JTT_DCMut+I 62 -2257.895 4639.791 2.973330e-34 4655.322
## 12 LG+G(4)+I 63 -2254.857 4635.714 2.283664e-33 4651.777
## 8 JTT+G(4)+I 63 -2255.785 4637.571 9.023447e-34 4653.634
## 60 Blosum62+G(4)+I 63 -2255.807 4637.614 8.828675e-34 4653.678
## 68 JTT_DCMut+G(4)+I 63 -2256.351 4638.702 5.124147e-34 4654.766
## 1 WAG 61 -2263.381 4648.762 3.351107e-36 4663.770
## 3 WAG+G(4) 62 -2260.337 4644.675 2.586405e-35 4660.206
## 2 WAG+I 62 -2261.887 4647.774 5.491625e-36 4663.305
## 4 WAG+G(4)+I 63 -2260.298 4646.597 9.894474e-36 4662.660
## 43 RtREV+G(4) 62 -2266.996 4657.991 3.319483e-38 4673.522
## 41 RtREV 61 -2270.525 4663.050 2.646470e-39 4678.058
## 42 RtREV+I 62 -2268.845 4661.690 5.223955e-39 4677.220
## 44 RtREV+G(4)+I 63 -2266.991 4659.982 1.226873e-38 4676.046
## 51 HIVb+G(4) 62 -2283.384 4690.768 2.533149e-45 4706.299
## 50 HIVb+I 62 -2284.819 4693.638 6.031978e-46 4709.169
## 54 FLU+I 62 -2285.155 4694.311 4.309048e-46 4709.842
## 55 FLU+G(4) 62 -2285.704 4695.408 2.489500e-46 4710.939
## 49 HIVb 61 -2288.961 4699.921 2.607059e-47 4714.929
## 53 FLU 61 -2288.970 4699.940 2.582352e-47 4714.948
## 14 Dayhoff+I 62 -2286.289 4696.578 1.387176e-46 4712.109
## 52 HIVb+G(4)+I 63 -2283.457 4692.914 8.662389e-46 4708.978
## 56 FLU+G(4)+I 63 -2284.923 4695.846 2.000513e-46 4711.909
## 21 mtmam 61 -2305.294 4732.587 2.102600e-54 4747.595
## 22 mtmam+I 62 -2302.664 4729.329 1.072519e-53 4744.859
## 23 mtmam+G(4) 62 -2304.277 4732.554 2.137519e-54 4748.085
## 24 mtmam+G(4)+I 63 -2302.695 4731.389 3.827892e-54 4747.453
## 47 HIVw+G(4) 62 -2339.832 4803.664 7.738658e-70 4819.195
## 61 Dayhoff_DCMut 61 -2344.547 4811.094 1.884843e-71 4826.102
## 13 Dayhoff 61 -2344.747 4811.493 1.543860e-71 4826.501
## 48 HIVw+G(4)+I 63 -2339.787 4805.574 2.977609e-70 4821.638
## 46 HIVw+I 62 -2343.931 4811.862 1.283894e-71 4827.393
## 63 Dayhoff_DCMut+G(4) 62 -2347.422 4818.845 3.910641e-73 4834.375
## 62 Dayhoff_DCMut+I 62 -2347.441 4818.882 3.838174e-73 4834.413
## 15 Dayhoff+G(4) 62 -2347.623 4819.246 3.199604e-73 4834.777
## 45 HIVw 61 -2352.958 4827.917 4.190232e-75 4842.925
## 64 Dayhoff_DCMut+G(4)+I 63 -2347.550 4821.101 1.265703e-73 4837.164
## 16 Dayhoff+G(4)+I 63 -2351.927 4829.853 1.591242e-75 4845.917
## AICcw BIC
## 31 6.696654e-01 4755.276
## 29 6.386385e-02 4756.161
## 30 7.295994e-02 4759.710
## 32 1.934962e-01 4761.565
## 27 8.943127e-06 4777.724
## 25 2.820172e-07 4780.821
## 35 1.283586e-06 4781.606
## 26 6.911406e-07 4782.844
## 28 2.961634e-06 4783.739
## 33 9.353731e-09 4787.634
## 36 3.617037e-07 4787.945
## 34 1.572362e-08 4790.410
## 19 6.148527e-27 4875.181
## 17 7.726615e-28 4875.514
## 18 4.689300e-28 4880.328
## 20 1.806498e-27 4881.437
## 39 1.249111e-30 4892.184
## 37 2.115418e-32 4896.525
## 40 3.519198e-31 4898.524
## 38 2.986603e-32 4899.651
## 57 1.091378e-33 4902.454
## 11 6.294533e-33 4902.766
## 7 2.562307e-33 4904.563
## 59 2.464880e-33 4904.641
## 9 2.413346e-34 4905.472
## 67 1.455063e-33 4905.695
## 10 1.121168e-33 4906.216
## 5 1.151975e-34 4906.951
## 6 5.508625e-34 4907.637
## 65 6.752978e-35 4908.020
## 58 4.292298e-34 4908.136
## 66 3.105320e-34 4908.784
## 12 1.827137e-33 4909.045
## 8 7.219571e-34 4910.902
## 60 7.063736e-34 4910.946
## 68 4.099779e-34 4912.034
## 1 4.545620e-36 4913.416
## 3 2.701218e-35 4913.668
## 2 5.735404e-36 4916.767
## 4 7.916471e-36 4919.928
## 43 3.466838e-38 4926.984
## 41 3.589813e-39 4927.704
## 42 5.455852e-39 4930.683
## 44 9.816090e-39 4933.314
## 51 2.645598e-45 4959.761
## 50 6.299744e-46 4962.631
## 54 4.500331e-46 4963.304
## 55 2.600012e-46 4964.401
## 49 3.536354e-47 4964.575
## 53 3.502839e-47 4964.594
## 14 1.448754e-46 4965.571
## 52 6.930691e-46 4966.246
## 56 1.600591e-46 4969.177
## 21 2.852079e-54 4997.242
## 22 1.120130e-53 4998.321
## 23 2.232406e-54 5001.547
## 24 3.062659e-54 5004.721
## 47 8.082185e-70 5072.657
## 61 2.556701e-71 5075.748
## 13 2.094174e-71 5076.147
## 48 2.382355e-70 5078.906
## 46 1.340888e-71 5080.855
## 63 4.084238e-73 5087.837
## 62 4.008554e-73 5087.875
## 15 3.341638e-73 5088.239
## 45 5.683853e-75 5092.571
## 64 1.012676e-73 5094.432
## 16 1.273137e-75 5103.185Meilleur modele: MtZoa+G(4)
env$`MtZoa+G(4)`## pml(tree = `tree_MtZoa+G(4)`, data = data, model = "MtZoa", k = 4,
## shape = 0.829019035772448)Trouver le meilleur modele
# Cadre 2
env <- attr(modelTest_aa_cadre2, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"modelTest_aa_cadre2[order(modelTest_aa_cadre2$AIC), ]## Model df logLik AIC AICw AICc
## 46 HIVw+I 62 -5101.986 10327.97 3.618698e-01 10343.72
## 48 HIVw+G(4)+I 63 -5100.988 10327.98 3.613028e-01 10344.27
## 47 HIVw+G(4) 62 -5102.354 10328.71 2.506855e-01 10344.46
## 45 HIVw 61 -5105.614 10333.23 2.614191e-02 10348.45
## 51 HIVb+G(4) 62 -5231.911 10587.82 1.358168e-57 10603.57
## 52 HIVb+G(4)+I 63 -5231.855 10589.71 5.285001e-58 10606.00
## 50 HIVb+I 62 -5235.771 10595.54 2.862673e-59 10611.29
## 49 HIVb 61 -5237.430 10596.86 1.480868e-59 10612.08
## 67 JTT_DCMut+G(4) 62 -5269.726 10663.45 5.129839e-74 10679.20
## 7 JTT+G(4) 62 -5270.491 10664.98 2.387255e-74 10680.73
## 68 JTT_DCMut+G(4)+I 63 -5269.558 10665.12 2.233081e-74 10681.41
## 66 JTT_DCMut+I 62 -5271.007 10666.01 1.425654e-74 10681.76
## 65 JTT_DCMut 61 -5272.287 10666.57 1.077425e-74 10681.79
## 8 JTT+G(4)+I 63 -5270.338 10666.68 1.023273e-74 10682.97
## 6 JTT+I 62 -5271.670 10667.34 7.342263e-75 10683.09
## 5 JTT 61 -5272.829 10667.66 6.263595e-75 10682.88
## 55 FLU+G(4) 62 -5323.252 10770.50 2.912942e-97 10786.25
## 56 FLU+G(4)+I 63 -5323.220 10772.44 1.105422e-97 10788.73
## 54 FLU+I 62 -5328.047 10780.09 2.408802e-99 10795.84
## 53 FLU 61 -5329.737 10781.47 1.208067e-99 10796.69
## 35 mtREV24+G(4) 62 -5453.626 11031.25 6.972729e-154 11047.00
## 36 mtREV24+G(4)+I 63 -5453.627 11033.25 2.561739e-154 11049.55
## 34 mtREV24+I 62 -5476.042 11076.08 1.282787e-163 11091.83
## 33 mtREV24 61 -5477.613 11077.23 7.249972e-164 11092.45
## 23 mtmam+G(4) 62 -5504.986 11133.97 3.451144e-176 11149.72
## 19 cpREV+G(4) 62 -5505.296 11134.59 2.532050e-176 11150.34
## 24 mtmam+G(4)+I 63 -5504.987 11135.97 1.269182e-176 11152.26
## 20 cpREV+G(4)+I 63 -5505.264 11136.53 9.619435e-177 11152.82
## 18 cpREV+I 62 -5515.340 11154.68 1.100233e-180 11170.43
## 17 cpREV 61 -5518.954 11159.91 8.059518e-182 11175.13
## 21 mtmam 61 -5520.483 11162.97 1.745870e-182 11178.19
## 22 mtmam+I 62 -5520.063 11164.13 9.775431e-183 11179.88
## 3 WAG+G(4) 62 -5565.296 11254.59 2.217907e-202 11270.34
## 4 WAG+G(4)+I 63 -5565.296 11256.59 8.158418e-203 11272.88
## 2 WAG+I 62 -5571.499 11267.00 4.485074e-205 11282.75
## 1 WAG 61 -5573.273 11268.55 2.068466e-205 11283.77
## 63 Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 4.786656e-241 11448.40
## 15 Dayhoff+G(4) 62 -5654.700 11433.40 3.297833e-241 11449.15
## 64 Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 2.135650e-241 11450.56
## 16 Dayhoff+G(4)+I 63 -5654.509 11435.02 1.467699e-241 11451.31
## 62 Dayhoff_DCMut+I 62 -5661.455 11446.91 3.840960e-244 11462.66
## 14 Dayhoff+I 62 -5661.948 11447.90 2.346654e-244 11463.65
## 61 Dayhoff_DCMut 61 -5666.022 11454.04 1.084507e-245 11469.26
## 13 Dayhoff 61 -5666.569 11455.14 6.274088e-246 11470.36
## 39 VT+G(4) 62 -5701.884 11527.77 1.062507e-261 11543.52
## 40 VT+G(4)+I 63 -5701.862 11529.72 3.994382e-262 11546.02
## 38 VT+I 62 -5713.168 11550.34 1.336383e-266 11566.09
## 37 VT 61 -5715.503 11553.01 3.516087e-267 11568.22
## 59 Blosum62+G(4) 62 -5717.550 11559.10 1.669218e-268 11574.85
## 60 Blosum62+G(4)+I 63 -5717.552 11561.10 6.133079e-269 11577.39
## 11 LG+G(4) 62 -5722.814 11569.63 8.637931e-271 11585.38
## 12 LG+G(4)+I 63 -5722.815 11571.63 3.176634e-271 11587.92
## 57 Blosum62 61 -5725.452 11572.90 1.679169e-271 11588.12
## 58 Blosum62+I 62 -5724.758 11573.52 1.236536e-271 11589.27
## 10 LG+I 62 -5732.276 11588.55 6.720733e-275 11604.30
## 9 LG 61 -5734.226 11590.45 2.597151e-275 11605.67
## 43 RtREV+G(4) 62 -5757.388 11638.78 8.342098e-286 11654.53
## 44 RtREV+G(4)+I 63 -5757.380 11640.76 3.093983e-286 11657.05
## 42 RtREV+I 62 -5770.184 11664.37 2.311155e-291 11680.12
## 41 RtREV 61 -5773.701 11669.40 1.865409e-292 11684.62
## 31 MtZoa+G(4) 62 -5780.309 11684.62 9.266275e-296 11700.37
## 32 MtZoa+G(4)+I 63 -5780.310 11686.62 3.405032e-296 11702.91
## 30 MtZoa+I 62 -5832.736 11789.47 1.577641e-318 11805.22
## 29 MtZoa 61 -5839.378 11800.76 5.592823e-321 11815.98
## 27 mtArt+G(4) 62 -5878.724 11881.45 0.000000e+00 11897.20
## 28 mtArt+G(4)+I 63 -5878.727 11883.45 0.000000e+00 11899.74
## 26 mtArt+I 62 -5976.513 12077.03 0.000000e+00 12092.78
## 25 mtArt 61 -5988.270 12098.54 0.000000e+00 12113.76
## AICcw BIC
## 46 3.923444e-01 10596.19
## 48 2.989025e-01 10600.52
## 47 2.717968e-01 10596.93
## 45 3.695634e-02 10597.12
## 51 1.472545e-57 10856.04
## 52 4.372233e-58 10862.26
## 50 3.103751e-59 10863.76
## 49 2.093477e-59 10860.75
## 67 5.561844e-74 10931.67
## 7 2.588296e-74 10933.20
## 68 1.847408e-74 10937.66
## 66 1.545714e-74 10934.23
## 65 1.523136e-74 10930.47
## 8 8.465441e-75 10939.22
## 6 7.960586e-75 10935.56
## 5 8.854732e-75 10931.55
## 55 3.158254e-97 11038.72
## 56 9.145058e-98 11044.99
## 54 2.611658e-99 11048.31
## 53 1.707823e-99 11045.37
## 35 7.559932e-154 11299.47
## 36 2.119303e-154 11305.80
## 34 1.390816e-163 11344.31
## 33 1.024915e-163 11341.12
## 23 3.741779e-176 11402.19
## 19 2.745285e-176 11402.81
## 24 1.049983e-176 11408.52
## 20 7.958070e-177 11409.07
## 18 1.192888e-180 11422.90
## 17 1.139360e-181 11423.80
## 21 2.468105e-182 11426.86
## 22 1.059866e-182 11432.35
## 3 2.404686e-202 11522.81
## 4 6.749384e-203 11529.14
## 2 4.862781e-205 11535.22
## 1 2.924153e-205 11532.44
## 63 5.189761e-241 11700.88
## 15 3.575557e-241 11701.62
## 64 1.766804e-241 11706.82
## 16 1.214214e-241 11707.57
## 62 4.164423e-244 11715.13
## 14 2.544276e-244 11716.12
## 61 1.533148e-245 11717.94
## 13 8.869565e-246 11719.03
## 39 1.151985e-261 11795.99
## 40 3.304516e-262 11802.27
## 38 1.448925e-266 11818.56
## 37 4.970629e-267 11816.90
## 59 1.809790e-268 11827.32
## 60 5.073839e-269 11833.65
## 11 9.365367e-271 11837.85
## 12 2.628000e-271 11844.18
## 57 2.373811e-271 11836.80
## 58 1.340670e-271 11841.74
## 10 7.286714e-275 11856.77
## 9 3.671545e-275 11854.35
## 43 9.044622e-286 11907.00
## 44 2.559623e-286 11913.31
## 42 2.505787e-291 11932.59
## 41 2.637096e-292 11933.30
## 31 1.004663e-295 11952.84
## 32 2.816951e-296 11959.17
## 30 1.710500e-318 12057.69
## 29 7.905050e-321 12064.65
## 27 0.000000e+00 12149.67
## 28 0.000000e+00 12156.00
## 26 0.000000e+00 12345.25
## 25 0.000000e+00 12362.44modelTest_aa_cadre2[order(modelTest_aa_cadre2$BIC), ]## Model df logLik AIC AICw AICc
## 46 HIVw+I 62 -5101.986 10327.97 3.618698e-01 10343.72
## 47 HIVw+G(4) 62 -5102.354 10328.71 2.506855e-01 10344.46
## 45 HIVw 61 -5105.614 10333.23 2.614191e-02 10348.45
## 48 HIVw+G(4)+I 63 -5100.988 10327.98 3.613028e-01 10344.27
## 51 HIVb+G(4) 62 -5231.911 10587.82 1.358168e-57 10603.57
## 49 HIVb 61 -5237.430 10596.86 1.480868e-59 10612.08
## 52 HIVb+G(4)+I 63 -5231.855 10589.71 5.285001e-58 10606.00
## 50 HIVb+I 62 -5235.771 10595.54 2.862673e-59 10611.29
## 65 JTT_DCMut 61 -5272.287 10666.57 1.077425e-74 10681.79
## 5 JTT 61 -5272.829 10667.66 6.263595e-75 10682.88
## 67 JTT_DCMut+G(4) 62 -5269.726 10663.45 5.129839e-74 10679.20
## 7 JTT+G(4) 62 -5270.491 10664.98 2.387255e-74 10680.73
## 66 JTT_DCMut+I 62 -5271.007 10666.01 1.425654e-74 10681.76
## 6 JTT+I 62 -5271.670 10667.34 7.342263e-75 10683.09
## 68 JTT_DCMut+G(4)+I 63 -5269.558 10665.12 2.233081e-74 10681.41
## 8 JTT+G(4)+I 63 -5270.338 10666.68 1.023273e-74 10682.97
## 55 FLU+G(4) 62 -5323.252 10770.50 2.912942e-97 10786.25
## 56 FLU+G(4)+I 63 -5323.220 10772.44 1.105422e-97 10788.73
## 53 FLU 61 -5329.737 10781.47 1.208067e-99 10796.69
## 54 FLU+I 62 -5328.047 10780.09 2.408802e-99 10795.84
## 35 mtREV24+G(4) 62 -5453.626 11031.25 6.972729e-154 11047.00
## 36 mtREV24+G(4)+I 63 -5453.627 11033.25 2.561739e-154 11049.55
## 33 mtREV24 61 -5477.613 11077.23 7.249972e-164 11092.45
## 34 mtREV24+I 62 -5476.042 11076.08 1.282787e-163 11091.83
## 23 mtmam+G(4) 62 -5504.986 11133.97 3.451144e-176 11149.72
## 19 cpREV+G(4) 62 -5505.296 11134.59 2.532050e-176 11150.34
## 24 mtmam+G(4)+I 63 -5504.987 11135.97 1.269182e-176 11152.26
## 20 cpREV+G(4)+I 63 -5505.264 11136.53 9.619435e-177 11152.82
## 18 cpREV+I 62 -5515.340 11154.68 1.100233e-180 11170.43
## 17 cpREV 61 -5518.954 11159.91 8.059518e-182 11175.13
## 21 mtmam 61 -5520.483 11162.97 1.745870e-182 11178.19
## 22 mtmam+I 62 -5520.063 11164.13 9.775431e-183 11179.88
## 3 WAG+G(4) 62 -5565.296 11254.59 2.217907e-202 11270.34
## 4 WAG+G(4)+I 63 -5565.296 11256.59 8.158418e-203 11272.88
## 1 WAG 61 -5573.273 11268.55 2.068466e-205 11283.77
## 2 WAG+I 62 -5571.499 11267.00 4.485074e-205 11282.75
## 63 Dayhoff_DCMut+G(4) 62 -5654.327 11432.65 4.786656e-241 11448.40
## 15 Dayhoff+G(4) 62 -5654.700 11433.40 3.297833e-241 11449.15
## 64 Dayhoff_DCMut+G(4)+I 63 -5654.134 11434.27 2.135650e-241 11450.56
## 16 Dayhoff+G(4)+I 63 -5654.509 11435.02 1.467699e-241 11451.31
## 62 Dayhoff_DCMut+I 62 -5661.455 11446.91 3.840960e-244 11462.66
## 14 Dayhoff+I 62 -5661.948 11447.90 2.346654e-244 11463.65
## 61 Dayhoff_DCMut 61 -5666.022 11454.04 1.084507e-245 11469.26
## 13 Dayhoff 61 -5666.569 11455.14 6.274088e-246 11470.36
## 39 VT+G(4) 62 -5701.884 11527.77 1.062507e-261 11543.52
## 40 VT+G(4)+I 63 -5701.862 11529.72 3.994382e-262 11546.02
## 37 VT 61 -5715.503 11553.01 3.516087e-267 11568.22
## 38 VT+I 62 -5713.168 11550.34 1.336383e-266 11566.09
## 59 Blosum62+G(4) 62 -5717.550 11559.10 1.669218e-268 11574.85
## 60 Blosum62+G(4)+I 63 -5717.552 11561.10 6.133079e-269 11577.39
## 57 Blosum62 61 -5725.452 11572.90 1.679169e-271 11588.12
## 11 LG+G(4) 62 -5722.814 11569.63 8.637931e-271 11585.38
## 58 Blosum62+I 62 -5724.758 11573.52 1.236536e-271 11589.27
## 12 LG+G(4)+I 63 -5722.815 11571.63 3.176634e-271 11587.92
## 9 LG 61 -5734.226 11590.45 2.597151e-275 11605.67
## 10 LG+I 62 -5732.276 11588.55 6.720733e-275 11604.30
## 43 RtREV+G(4) 62 -5757.388 11638.78 8.342098e-286 11654.53
## 44 RtREV+G(4)+I 63 -5757.380 11640.76 3.093983e-286 11657.05
## 42 RtREV+I 62 -5770.184 11664.37 2.311155e-291 11680.12
## 41 RtREV 61 -5773.701 11669.40 1.865409e-292 11684.62
## 31 MtZoa+G(4) 62 -5780.309 11684.62 9.266275e-296 11700.37
## 32 MtZoa+G(4)+I 63 -5780.310 11686.62 3.405032e-296 11702.91
## 30 MtZoa+I 62 -5832.736 11789.47 1.577641e-318 11805.22
## 29 MtZoa 61 -5839.378 11800.76 5.592823e-321 11815.98
## 27 mtArt+G(4) 62 -5878.724 11881.45 0.000000e+00 11897.20
## 28 mtArt+G(4)+I 63 -5878.727 11883.45 0.000000e+00 11899.74
## 26 mtArt+I 62 -5976.513 12077.03 0.000000e+00 12092.78
## 25 mtArt 61 -5988.270 12098.54 0.000000e+00 12113.76
## AICcw BIC
## 46 3.923444e-01 10596.19
## 47 2.717968e-01 10596.93
## 45 3.695634e-02 10597.12
## 48 2.989025e-01 10600.52
## 51 1.472545e-57 10856.04
## 49 2.093477e-59 10860.75
## 52 4.372233e-58 10862.26
## 50 3.103751e-59 10863.76
## 65 1.523136e-74 10930.47
## 5 8.854732e-75 10931.55
## 67 5.561844e-74 10931.67
## 7 2.588296e-74 10933.20
## 66 1.545714e-74 10934.23
## 6 7.960586e-75 10935.56
## 68 1.847408e-74 10937.66
## 8 8.465441e-75 10939.22
## 55 3.158254e-97 11038.72
## 56 9.145058e-98 11044.99
## 53 1.707823e-99 11045.37
## 54 2.611658e-99 11048.31
## 35 7.559932e-154 11299.47
## 36 2.119303e-154 11305.80
## 33 1.024915e-163 11341.12
## 34 1.390816e-163 11344.31
## 23 3.741779e-176 11402.19
## 19 2.745285e-176 11402.81
## 24 1.049983e-176 11408.52
## 20 7.958070e-177 11409.07
## 18 1.192888e-180 11422.90
## 17 1.139360e-181 11423.80
## 21 2.468105e-182 11426.86
## 22 1.059866e-182 11432.35
## 3 2.404686e-202 11522.81
## 4 6.749384e-203 11529.14
## 1 2.924153e-205 11532.44
## 2 4.862781e-205 11535.22
## 63 5.189761e-241 11700.88
## 15 3.575557e-241 11701.62
## 64 1.766804e-241 11706.82
## 16 1.214214e-241 11707.57
## 62 4.164423e-244 11715.13
## 14 2.544276e-244 11716.12
## 61 1.533148e-245 11717.94
## 13 8.869565e-246 11719.03
## 39 1.151985e-261 11795.99
## 40 3.304516e-262 11802.27
## 37 4.970629e-267 11816.90
## 38 1.448925e-266 11818.56
## 59 1.809790e-268 11827.32
## 60 5.073839e-269 11833.65
## 57 2.373811e-271 11836.80
## 11 9.365367e-271 11837.85
## 58 1.340670e-271 11841.74
## 12 2.628000e-271 11844.18
## 9 3.671545e-275 11854.35
## 10 7.286714e-275 11856.77
## 43 9.044622e-286 11907.00
## 44 2.559623e-286 11913.31
## 42 2.505787e-291 11932.59
## 41 2.637096e-292 11933.30
## 31 1.004663e-295 11952.84
## 32 2.816951e-296 11959.17
## 30 1.710500e-318 12057.69
## 29 7.905050e-321 12064.65
## 27 0.000000e+00 12149.67
## 28 0.000000e+00 12156.00
## 26 0.000000e+00 12345.25
## 25 0.000000e+00 12362.44Meilleur modele: HIVw+I
env$`HIVw+I`## pml(tree = `tree_HIVw+I`, data = data, model = "HIVw", inv = 0.031773228237453)Trouver le meilleur modele
# Cadre 3
env <- attr(modelTest_aa_cadre3, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"modelTest_aa_cadre3[order(modelTest_aa_cadre3$AIC), ]## Model df logLik AIC AICw AICc
## 47 HIVw+G(4) 62 -5274.747 10673.49 6.649646e-01 10690.11
## 48 HIVw+G(4)+I 63 -5274.432 10674.86 3.350351e-01 10692.06
## 46 HIVw+I 62 -5289.262 10702.52 3.303761e-07 10719.14
## 45 HIVw 61 -5296.140 10714.28 9.249019e-10 10730.34
## 23 mtmam+G(4) 62 -5348.536 10821.07 5.978047e-33 10837.69
## 7 JTT+G(4) 62 -5348.833 10821.67 4.440953e-33 10838.29
## 24 mtmam+G(4)+I 63 -5348.536 10823.07 2.198422e-33 10840.27
## 8 JTT+G(4)+I 63 -5348.822 10823.64 1.651017e-33 10840.84
## 6 JTT+I 62 -5357.455 10838.91 7.994553e-37 10855.53
## 67 JTT_DCMut+G(4) 62 -5357.833 10839.67 5.480540e-37 10856.29
## 68 JTT_DCMut+G(4)+I 63 -5357.824 10841.65 2.034288e-37 10858.84
## 5 JTT 61 -5360.294 10842.59 1.271439e-37 10858.65
## 66 JTT_DCMut+I 62 -5366.753 10857.51 7.329049e-41 10874.13
## 65 JTT_DCMut 61 -5369.642 10861.28 1.107470e-41 10877.34
## 55 FLU+G(4) 62 -5372.332 10868.66 2.765310e-43 10885.29
## 56 FLU+G(4)+I 63 -5372.299 10870.60 1.052343e-43 10887.79
## 21 mtmam 61 -5378.721 10879.44 1.263591e-45 10895.50
## 22 mtmam+I 62 -5377.876 10879.75 1.081641e-45 10896.37
## 51 HIVb+G(4) 62 -5386.722 10897.44 1.558350e-49 10914.06
## 52 HIVb+G(4)+I 63 -5386.720 10899.44 5.739467e-50 10916.63
## 54 FLU+I 62 -5398.516 10921.03 1.176533e-54 10937.65
## 50 HIVb+I 62 -5403.549 10931.10 7.665060e-57 10947.72
## 53 FLU 61 -5404.973 10931.95 5.019241e-57 10948.00
## 49 HIVb 61 -5408.020 10938.04 2.383360e-58 10954.10
## 35 mtREV24+G(4) 62 -5437.664 10999.33 1.171223e-71 11015.95
## 36 mtREV24+G(4)+I 63 -5437.664 11001.33 4.307466e-72 11018.52
## 19 cpREV+G(4) 62 -5448.791 11021.58 1.722105e-76 11038.20
## 20 cpREV+G(4)+I 63 -5448.787 11023.57 6.364079e-77 11040.77
## 18 cpREV+I 62 -5470.870 11065.74 4.442382e-86 11082.36
## 34 mtREV24+I 62 -5475.823 11075.65 3.136497e-88 11092.27
## 17 cpREV 61 -5477.362 11076.72 1.830085e-88 11092.78
## 33 mtREV24 61 -5482.664 11087.33 9.109128e-91 11103.39
## 3 WAG+G(4) 62 -5541.009 11206.02 1.536086e-116 11222.64
## 4 WAG+G(4)+I 63 -5541.007 11208.01 5.662926e-117 11225.21
## 2 WAG+I 62 -5551.780 11227.56 3.226686e-121 11244.18
## 1 WAG 61 -5555.198 11232.40 2.874643e-122 11248.46
## 31 MtZoa+G(4) 62 -5563.323 11250.65 3.129609e-126 11267.27
## 32 MtZoa+G(4)+I 63 -5563.324 11252.65 1.150247e-126 11269.84
## 11 LG+G(4) 62 -5596.215 11316.43 1.625238e-140 11333.05
## 12 LG+G(4)+I 63 -5596.215 11318.43 5.978652e-141 11335.62
## 10 LG+I 62 -5610.756 11345.51 7.862243e-147 11362.13
## 9 LG 61 -5614.854 11351.71 3.549742e-148 11367.77
## 63 Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 6.448031e-151 11380.95
## 15 Dayhoff+G(4) 62 -5620.341 11364.68 5.406281e-151 11381.30
## 64 Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 2.213188e-151 11383.66
## 16 Dayhoff+G(4)+I 63 -5620.411 11366.82 1.854652e-151 11384.02
## 30 MtZoa+I 62 -5623.709 11371.42 1.864032e-152 11388.04
## 29 MtZoa 61 -5631.963 11385.93 1.317894e-155 11401.99
## 62 Dayhoff_DCMut+I 62 -5637.732 11399.46 1.514287e-158 11416.09
## 14 Dayhoff+I 62 -5638.096 11400.19 1.052591e-158 11416.81
## 61 Dayhoff_DCMut 61 -5641.668 11405.34 8.034959e-160 11421.40
## 13 Dayhoff 61 -5642.067 11406.13 5.393946e-160 11422.19
## 59 Blosum62+G(4) 62 -5715.334 11554.67 3.006953e-192 11571.29
## 60 Blosum62+G(4)+I 63 -5715.306 11556.61 1.137461e-192 11573.81
## 58 Blosum62+I 62 -5725.072 11574.14 1.774557e-196 11590.76
## 57 Blosum62 61 -5729.070 11580.14 8.846016e-198 11596.20
## 27 mtArt+G(4) 62 -5735.987 11595.97 3.224239e-201 11612.60
## 28 mtArt+G(4)+I 63 -5735.988 11597.98 1.184936e-201 11615.17
## 43 RtREV+G(4) 62 -5739.590 11603.18 8.785025e-203 11619.80
## 44 RtREV+G(4)+I 63 -5739.561 11605.12 3.329035e-203 11622.32
## 42 RtREV+I 62 -5754.169 11632.34 4.095275e-209 11648.96
## 41 RtREV 61 -5758.647 11639.29 1.263904e-210 11655.35
## 39 VT+G(4) 62 -5802.941 11729.88 2.696092e-230 11746.50
## 40 VT+G(4)+I 63 -5802.941 11731.88 9.917304e-231 11749.08
## 26 mtArt+I 62 -5825.196 11774.39 5.828761e-240 11791.01
## 25 mtArt 61 -5837.166 11796.33 1.003662e-244 11812.39
## 38 VT+I 62 -5844.255 11812.51 3.077697e-248 11829.13
## 37 VT 61 -5856.713 11835.43 3.251560e-253 11851.49
## AICcw BIC
## 47 7.254928e-01 10938.76
## 48 2.745068e-01 10944.41
## 46 3.604485e-07 10967.79
## 45 1.336380e-09 10975.27
## 23 6.522197e-33 11086.34
## 7 4.845190e-33 11086.93
## 24 1.801250e-33 11092.62
## 8 1.352740e-33 11093.19
## 6 8.722255e-37 11104.18
## 67 5.979405e-37 11104.93
## 68 1.666768e-37 11111.19
## 5 1.837086e-37 11103.58
## 66 7.996174e-41 11122.77
## 65 1.600170e-41 11122.27
## 55 3.017021e-43 11133.93
## 56 8.622239e-44 11140.14
## 21 1.825747e-45 11140.43
## 22 1.180097e-45 11145.02
## 51 1.700198e-49 11162.71
## 52 4.702561e-50 11168.99
## 54 1.283627e-54 11186.30
## 50 8.362770e-57 11196.37
## 53 7.252240e-57 11192.93
## 49 3.443689e-58 11199.03
## 35 1.277833e-71 11264.60
## 36 3.529268e-72 11270.88
## 19 1.878859e-76 11286.85
## 20 5.214329e-77 11293.12
## 18 4.846749e-86 11331.01
## 34 3.421996e-88 11340.91
## 17 2.644268e-88 11337.71
## 33 1.316167e-90 11348.32
## 3 1.675907e-116 11471.29
## 4 4.639848e-117 11477.56
## 2 3.520395e-121 11492.83
## 1 4.153537e-122 11493.39
## 31 3.414481e-126 11515.91
## 32 9.424404e-127 11522.20
## 11 1.773175e-140 11581.70
## 12 4.898533e-141 11587.98
## 10 8.577902e-147 11610.78
## 9 5.128979e-148 11612.70
## 63 7.034961e-151 11629.60
## 15 5.898387e-151 11629.95
## 64 1.813348e-151 11636.02
## 16 1.519586e-151 11636.37
## 30 2.033705e-152 11636.69
## 29 1.904210e-155 11646.92
## 62 1.652125e-158 11664.73
## 14 1.148403e-158 11665.46
## 61 1.160962e-159 11666.33
## 13 7.793648e-160 11667.12
## 59 3.280660e-192 11819.94
## 60 9.319641e-193 11826.16
## 58 1.936085e-196 11839.41
## 57 1.278150e-197 11841.13
## 27 3.517725e-201 11861.24
## 28 9.708622e-202 11867.52
## 43 9.584680e-203 11868.45
## 44 2.727603e-203 11874.67
## 42 4.468047e-209 11897.61
## 41 1.826200e-210 11900.28
## 39 2.941503e-230 11995.15
## 40 8.125619e-231 12001.43
## 26 6.359322e-240 12039.66
## 25 1.450179e-244 12057.32
## 38 3.357843e-248 12077.78
## 37 4.698140e-253 12096.42modelTest_aa_cadre3[order(modelTest_aa_cadre3$BIC), ]## Model df logLik AIC AICw AICc
## 47 HIVw+G(4) 62 -5274.747 10673.49 6.649646e-01 10690.11
## 48 HIVw+G(4)+I 63 -5274.432 10674.86 3.350351e-01 10692.06
## 46 HIVw+I 62 -5289.262 10702.52 3.303761e-07 10719.14
## 45 HIVw 61 -5296.140 10714.28 9.249019e-10 10730.34
## 23 mtmam+G(4) 62 -5348.536 10821.07 5.978047e-33 10837.69
## 7 JTT+G(4) 62 -5348.833 10821.67 4.440953e-33 10838.29
## 24 mtmam+G(4)+I 63 -5348.536 10823.07 2.198422e-33 10840.27
## 8 JTT+G(4)+I 63 -5348.822 10823.64 1.651017e-33 10840.84
## 5 JTT 61 -5360.294 10842.59 1.271439e-37 10858.65
## 6 JTT+I 62 -5357.455 10838.91 7.994553e-37 10855.53
## 67 JTT_DCMut+G(4) 62 -5357.833 10839.67 5.480540e-37 10856.29
## 68 JTT_DCMut+G(4)+I 63 -5357.824 10841.65 2.034288e-37 10858.84
## 65 JTT_DCMut 61 -5369.642 10861.28 1.107470e-41 10877.34
## 66 JTT_DCMut+I 62 -5366.753 10857.51 7.329049e-41 10874.13
## 55 FLU+G(4) 62 -5372.332 10868.66 2.765310e-43 10885.29
## 56 FLU+G(4)+I 63 -5372.299 10870.60 1.052343e-43 10887.79
## 21 mtmam 61 -5378.721 10879.44 1.263591e-45 10895.50
## 22 mtmam+I 62 -5377.876 10879.75 1.081641e-45 10896.37
## 51 HIVb+G(4) 62 -5386.722 10897.44 1.558350e-49 10914.06
## 52 HIVb+G(4)+I 63 -5386.720 10899.44 5.739467e-50 10916.63
## 54 FLU+I 62 -5398.516 10921.03 1.176533e-54 10937.65
## 53 FLU 61 -5404.973 10931.95 5.019241e-57 10948.00
## 50 HIVb+I 62 -5403.549 10931.10 7.665060e-57 10947.72
## 49 HIVb 61 -5408.020 10938.04 2.383360e-58 10954.10
## 35 mtREV24+G(4) 62 -5437.664 10999.33 1.171223e-71 11015.95
## 36 mtREV24+G(4)+I 63 -5437.664 11001.33 4.307466e-72 11018.52
## 19 cpREV+G(4) 62 -5448.791 11021.58 1.722105e-76 11038.20
## 20 cpREV+G(4)+I 63 -5448.787 11023.57 6.364079e-77 11040.77
## 18 cpREV+I 62 -5470.870 11065.74 4.442382e-86 11082.36
## 17 cpREV 61 -5477.362 11076.72 1.830085e-88 11092.78
## 34 mtREV24+I 62 -5475.823 11075.65 3.136497e-88 11092.27
## 33 mtREV24 61 -5482.664 11087.33 9.109128e-91 11103.39
## 3 WAG+G(4) 62 -5541.009 11206.02 1.536086e-116 11222.64
## 4 WAG+G(4)+I 63 -5541.007 11208.01 5.662926e-117 11225.21
## 2 WAG+I 62 -5551.780 11227.56 3.226686e-121 11244.18
## 1 WAG 61 -5555.198 11232.40 2.874643e-122 11248.46
## 31 MtZoa+G(4) 62 -5563.323 11250.65 3.129609e-126 11267.27
## 32 MtZoa+G(4)+I 63 -5563.324 11252.65 1.150247e-126 11269.84
## 11 LG+G(4) 62 -5596.215 11316.43 1.625238e-140 11333.05
## 12 LG+G(4)+I 63 -5596.215 11318.43 5.978652e-141 11335.62
## 10 LG+I 62 -5610.756 11345.51 7.862243e-147 11362.13
## 9 LG 61 -5614.854 11351.71 3.549742e-148 11367.77
## 63 Dayhoff_DCMut+G(4) 62 -5620.165 11364.33 6.448031e-151 11380.95
## 15 Dayhoff+G(4) 62 -5620.341 11364.68 5.406281e-151 11381.30
## 64 Dayhoff_DCMut+G(4)+I 63 -5620.234 11366.47 2.213188e-151 11383.66
## 16 Dayhoff+G(4)+I 63 -5620.411 11366.82 1.854652e-151 11384.02
## 30 MtZoa+I 62 -5623.709 11371.42 1.864032e-152 11388.04
## 29 MtZoa 61 -5631.963 11385.93 1.317894e-155 11401.99
## 62 Dayhoff_DCMut+I 62 -5637.732 11399.46 1.514287e-158 11416.09
## 14 Dayhoff+I 62 -5638.096 11400.19 1.052591e-158 11416.81
## 61 Dayhoff_DCMut 61 -5641.668 11405.34 8.034959e-160 11421.40
## 13 Dayhoff 61 -5642.067 11406.13 5.393946e-160 11422.19
## 59 Blosum62+G(4) 62 -5715.334 11554.67 3.006953e-192 11571.29
## 60 Blosum62+G(4)+I 63 -5715.306 11556.61 1.137461e-192 11573.81
## 58 Blosum62+I 62 -5725.072 11574.14 1.774557e-196 11590.76
## 57 Blosum62 61 -5729.070 11580.14 8.846016e-198 11596.20
## 27 mtArt+G(4) 62 -5735.987 11595.97 3.224239e-201 11612.60
## 28 mtArt+G(4)+I 63 -5735.988 11597.98 1.184936e-201 11615.17
## 43 RtREV+G(4) 62 -5739.590 11603.18 8.785025e-203 11619.80
## 44 RtREV+G(4)+I 63 -5739.561 11605.12 3.329035e-203 11622.32
## 42 RtREV+I 62 -5754.169 11632.34 4.095275e-209 11648.96
## 41 RtREV 61 -5758.647 11639.29 1.263904e-210 11655.35
## 39 VT+G(4) 62 -5802.941 11729.88 2.696092e-230 11746.50
## 40 VT+G(4)+I 63 -5802.941 11731.88 9.917304e-231 11749.08
## 26 mtArt+I 62 -5825.196 11774.39 5.828761e-240 11791.01
## 25 mtArt 61 -5837.166 11796.33 1.003662e-244 11812.39
## 38 VT+I 62 -5844.255 11812.51 3.077697e-248 11829.13
## 37 VT 61 -5856.713 11835.43 3.251560e-253 11851.49
## AICcw BIC
## 47 7.254928e-01 10938.76
## 48 2.745068e-01 10944.41
## 46 3.604485e-07 10967.79
## 45 1.336380e-09 10975.27
## 23 6.522197e-33 11086.34
## 7 4.845190e-33 11086.93
## 24 1.801250e-33 11092.62
## 8 1.352740e-33 11093.19
## 5 1.837086e-37 11103.58
## 6 8.722255e-37 11104.18
## 67 5.979405e-37 11104.93
## 68 1.666768e-37 11111.19
## 65 1.600170e-41 11122.27
## 66 7.996174e-41 11122.77
## 55 3.017021e-43 11133.93
## 56 8.622239e-44 11140.14
## 21 1.825747e-45 11140.43
## 22 1.180097e-45 11145.02
## 51 1.700198e-49 11162.71
## 52 4.702561e-50 11168.99
## 54 1.283627e-54 11186.30
## 53 7.252240e-57 11192.93
## 50 8.362770e-57 11196.37
## 49 3.443689e-58 11199.03
## 35 1.277833e-71 11264.60
## 36 3.529268e-72 11270.88
## 19 1.878859e-76 11286.85
## 20 5.214329e-77 11293.12
## 18 4.846749e-86 11331.01
## 17 2.644268e-88 11337.71
## 34 3.421996e-88 11340.91
## 33 1.316167e-90 11348.32
## 3 1.675907e-116 11471.29
## 4 4.639848e-117 11477.56
## 2 3.520395e-121 11492.83
## 1 4.153537e-122 11493.39
## 31 3.414481e-126 11515.91
## 32 9.424404e-127 11522.20
## 11 1.773175e-140 11581.70
## 12 4.898533e-141 11587.98
## 10 8.577902e-147 11610.78
## 9 5.128979e-148 11612.70
## 63 7.034961e-151 11629.60
## 15 5.898387e-151 11629.95
## 64 1.813348e-151 11636.02
## 16 1.519586e-151 11636.37
## 30 2.033705e-152 11636.69
## 29 1.904210e-155 11646.92
## 62 1.652125e-158 11664.73
## 14 1.148403e-158 11665.46
## 61 1.160962e-159 11666.33
## 13 7.793648e-160 11667.12
## 59 3.280660e-192 11819.94
## 60 9.319641e-193 11826.16
## 58 1.936085e-196 11839.41
## 57 1.278150e-197 11841.13
## 27 3.517725e-201 11861.24
## 28 9.708622e-202 11867.52
## 43 9.584680e-203 11868.45
## 44 2.727603e-203 11874.67
## 42 4.468047e-209 11897.61
## 41 1.826200e-210 11900.28
## 39 2.941503e-230 11995.15
## 40 8.125619e-231 12001.43
## 26 6.359322e-240 12039.66
## 25 1.450179e-244 12057.32
## 38 3.357843e-248 12077.78
## 37 4.698140e-253 12096.42Meilleur modele: HIVw+G(4)
env$`HIVw+G(4)`## pml(tree = `tree_HIVw+G(4)`, data = data, model = "HIVw", k = 4,
## shape = 3.18746367818674)ii) Reconstruire les arbres phylogénétiques (prédits par modelTest()) à l’aide d’une analyse bootstrap (itérations = 1000).
Matrice de distances
# Cadre 1
dm_cadre1 <- dist.ml(Align_aa_cadre1_phangorn, model = "MtZoa")
# Cadre 2
dm_cadre2 <- dist.ml(Align_aa_cadre2_phangorn, model = "HIVw")
# Cadre 3
dm_cadre3 <- dist.ml(Align_aa_cadre3_phangorn, model = "HIVw")Construction d’arbre par NJ
# Cadre 1
treeNJ_cadre1 <- NJ(dm_cadre1)
# Cadre 2
treeNJ_cadre2 <- NJ(dm_cadre2)
# Cadre 3
treeNJ_cadre3 <- NJ(dm_cadre3)Integration des parametres
# Cadre 1
fit_cadre1 = pml(treeNJ_cadre1, data=Align_aa_cadre1_phangorn)
fitmodel_cadre1 <- update(fit_cadre1, model="MtZoa", k = 4, shape = 0.831043307700432)
fitmodel_cadre1 <- optim.pml(fitmodel_cadre1, model="MtZoa", optShape = TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
# Cadre 2
fit_cadre2 = pml(treeNJ_cadre2, data=Align_aa_cadre2_phangorn)
fitmodel_cadre2 <- update(fit_cadre2, model="HIVw", inv= 0.0317733315974381)
fitmodel_cadre2 <- optim.pml(fitmodel_cadre2, model="HIVw", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))
# Cadre 3
fit_cadre3 = pml(treeNJ_cadre3, data=Align_aa_cadre3_phangorn)
fitmodel_cadre3 <- update(fit_cadre3, model="HIVw", k = 4, shape = 3.19289035895832)
fitmodel_cadre3 <- optim.pml(fitmodel_cadre3, model="HIVw", optShape=TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap sans correction
# Cadre 1
boot_cadre1 <- bootstrap.phyDat(Align_aa_cadre1_phangorn, FUN = function(x) NJ(dist.ml(x, model = "MtZoa")), bs = 1000)cons_boot_cadre1 <- consensus(boot_cadre1, p= 0.5)
plot(cons_boot_cadre1, main = "Bootstrap avec MtZoa pour la cadre 1", no.margin = TRUE)
nodelabels(cons_boot_cadre1$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
# Cadre 2
boot_cadre2 <- bootstrap.phyDat(Align_aa_cadre2_phangorn, FUN = function(x) NJ(dist.ml(x, model = "HIVw")), bs = 1000)cons_boot_cadre2 <- consensus(boot_cadre2, p= 0.5)
plot(cons_boot_cadre2, main = "Bootstrap avec HIVw pour la cadre 2", no.margin = TRUE)
nodelabels(cons_boot_cadre2$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
# Cadre 3
boot_cadre3 <- bootstrap.phyDat(Align_aa_cadre3_phangorn, FUN = function(x) NJ(dist.ml(x, model = "HIVw")), bs = 1000)cons_boot_cadre3 <- consensus(boot_cadre3, p= 0.5)
plot(cons_boot_cadre3, main = "Bootstrap avec HIVw pour la cadre 3", no.margin = TRUE)
nodelabels(cons_boot_cadre3$node.label * 100,
bg = "white",
frame = "circle", cex = 0.6)
Analyse bootstrap avec correction
# Cadre 1
boot_cadre1 = bootstrap.pml(fitmodel_cadre1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre1$tree), boot_cadre1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
# Cadre 2
boot_cadre2 = bootstrap.pml(fitmodel_cadre2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre2$tree), boot_cadre2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
# Cadre 3
boot_cadre3 = bootstrap.pml(fitmodel_cadre3, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
plotBS(midpoint(fitmodel_cadre3$tree), boot_cadre3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
F) Rechercher dans NCBI d’autres groupes externes pour le gène COI : (Lamantin + Dugong = Siréniens, l’éléphant d’Afrique + d’Asie, hippopotame + hippopotame nain et [Tortue luth +
Cistude] les ajouter au jeu de donné. Essayer les quatre paires séparément, et ensemble. (ADN et AA)
Modifier les jeux de donnees
##Enlever hippopotame + groupe externe de sequence
myNewSequences <- mySequences[!names(mySequences) %in% c("5836030", "5835009", "157058317", "157058315", "157058313", "157058311", "157058355")]
#Importer le fichier groupe_externe.txt
myExterneSequences <- readDNAStringSet("groupe_externe.txt", format = "fasta")
names(myExterneSequences) <- sub("(^\\S+).*", "\\1", names(myExterneSequences))Lamantin + Dugong = Siréniens
Code NCBI: - HQ918430.1 Trichechus manatus voucher - KF430645.1 Dugong dugon voucher
Fusionner avec les cetaces
Sequences_groupe_externe_1 <- c(myNewSequences, myExterneSequences[1:2])ADN
Alignement
mySequences_align_gr_ext_1 = AlignSeqs(Sequences_groupe_externe_1, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Alignment converged - skipping remaining iteration.Recherche du meilleur modele
mySequences_align_gr_ext_1_ape = as.DNAbin(mySequences_align_gr_ext_1)
mySequences_align_gr_ext_1_phangorn = as.phyDat(mySequences_align_gr_ext_1_ape)
mySequences_gr_ext_1_modelTest = phangorn::modelTest(mySequences_align_gr_ext_1_phangorn)## Model df logLik AIC BIC
## JC 51 -4344.147 8790.293 9019.243
## JC+I 52 -4059.86 8223.72 8457.158
## JC+G(4) 52 -4068.427 8240.854 8474.293
## JC+G(4)+I 53 -4058.196 8222.392 8460.32
## F81 54 -4314.488 8736.975 8979.392
## F81+I 55 -4017.012 8144.023 8390.929
## F81+G(4) 55 -4024.227 8158.455 8405.361
## F81+G(4)+I 56 -4014.507 8141.014 8392.41
## K80 52 -4009.619 8123.239 8356.677
## K80+I 53 -3660.084 7426.167 7664.095
## K80+G(4) 53 -3669.183 7444.365 7682.293
## K80+G(4)+I 54 -3656.492 7420.984 7663.401
## HKY 55 -3980.945 8071.89 8318.797
## HKY+I 56 -3602.499 7316.999 7568.394
## HKY+G(4) 56 -3617.671 7347.343 7598.738
## HKY+G(4)+I 57 -3599.94 7313.879 7569.764
## TrNe 53 -3982.48 8070.961 8308.889
## TrNe+I 54 -3636.827 7381.654 7624.072
## TrNe+G(4) 54 -3650.48 7408.96 7651.377
## TrNe+G(4)+I 55 -3632.633 7375.265 7622.171
## TrN 56 -3973.238 8058.476 8309.871
## TrN+I 57 -3600.693 7315.386 7571.27
## TrN+G(4) 57 -3615.921 7345.843 7601.727
## TrN+G(4)+I 58 -3597.709 7311.418 7571.792
## TPM1 53 -4009.619 8125.238 8363.166
## TPM1+I 54 -3659.721 7427.442 7669.859
## TPM1+G(4) 54 -3668.589 7445.178 7687.595
## TPM1+G(4)+I 55 -3655.97 7421.939 7668.845
## K81 53 -4009.619 8125.238 8363.166
## K81+I 54 -3659.721 7427.442 7669.859
## K81+G(4) 54 -3668.589 7445.178 7687.595
## K81+G(4)+I 55 -3655.97 7421.939 7668.845
## TPM1u 56 -3980.936 8073.872 8325.268
## TPM1u+I 57 -3601.942 7317.884 7573.769
## TPM1u+G(4) 57 -3616.896 7347.793 7603.677
## TPM1u+G(4)+I 58 -3599.252 7314.503 7574.877
## TPM2 53 -3978.025 8062.049 8299.977
## TPM2+I 54 -3652.455 7412.91 7655.327
## TPM2+G(4) 54 -3657.53 7423.059 7665.476
## TPM2+G(4)+I 55 -3647.626 7405.252 7652.158
## TPM2u 56 -3959.441 8030.882 8282.278
## TPM2u+I 57 -3599.831 7313.662 7569.547
## TPM2u+G(4) 57 -3614.478 7342.956 7598.841
## TPM2u+G(4)+I 58 -3597.244 7310.489 7570.863
## TPM3 53 -4009.324 8124.648 8362.576
## TPM3+I 54 -3653.62 7415.239 7657.656
## TPM3+G(4) 54 -3664.871 7437.742 7680.159
## TPM3+G(4)+I 55 -3649.949 7409.897 7656.804
## TPM3u 56 -3980.797 8073.594 8324.989
## TPM3u+I 57 -3596.915 7307.831 7563.715
## TPM3u+G(4) 57 -3613.728 7341.455 7597.34
## TPM3u+G(4)+I 58 -3594.204 7304.409 7564.783
## TIM1e 54 -3982.48 8072.96 8315.377
## TIM1e+I 55 -3636.449 7382.897 7629.803
## TIM1e+G(4) 55 -3649.767 7409.533 7656.44
## TIM1e+G(4)+I 56 -3632.112 7376.224 7627.62
## TIM1 57 -3973.229 8060.459 8316.343
## TIM1+I 58 -3600.137 7316.274 7576.648
## TIM1+G(4) 58 -3615.119 7346.238 7606.612
## TIM1+G(4)+I 59 -3597.02 7312.04 7576.903
## TIM2e 54 -3950.763 8009.526 8251.943
## TIM2e+I 55 -3626.819 7363.638 7610.544
## TIM2e+G(4) 55 -3638.398 7386.796 7633.702
## TIM2e+G(4)+I 56 -3621.474 7354.948 7606.344
## TIM2 57 -3951.784 8017.568 8273.453
## TIM2+I 58 -3597.782 7311.564 7571.938
## TIM2+G(4) 58 -3612.49 7340.98 7601.354
## TIM2+G(4)+I 59 -3594.73 7307.461 7572.324
## TIM3e 54 -3982.132 8072.264 8314.681
## TIM3e+I 55 -3629.973 7369.946 7616.852
## TIM3e+G(4) 55 -3645.669 7401.338 7648.244
## TIM3e+G(4)+I 56 -3625.53 7363.06 7614.455
## TIM3 57 -3973.069 8060.138 8316.023
## TIM3+I 58 -3594.999 7305.997 7566.371
## TIM3+G(4) 58 -3611.859 7339.717 7600.091
## TIM3+G(4)+I 59 -3591.802 7301.604 7566.467
## TVMe 55 -3976.644 8063.287 8310.194
## TVMe+I 56 -3645.028 7402.056 7653.452
## TVMe+G(4) 56 -3652.83 7417.659 7669.055
## TVMe+G(4)+I 57 -3640.697 7395.394 7651.278
## TVM 58 -3958.2 8032.401 8292.775
## TVM+I 59 -3593.031 7304.062 7568.925
## TVM+G(4) 59 -3610.178 7338.357 7603.22
## TVM+G(4)+I 60 -3590.584 7301.169 7570.521
## SYM 56 -3949.43 8010.86 8262.256
## SYM+I 57 -3619.025 7352.05 7607.935
## SYM+G(4) 57 -3633.334 7380.668 7636.552
## SYM+G(4)+I 58 -3614.117 7344.235 7604.609
## GTR 59 -3950.578 8019.156 8284.019
## GTR+I 60 -3590.889 7301.778 7571.13
## GTR+G(4) 60 -3608.088 7336.176 7605.528
## GTR+G(4)+I 61 -3587.971 7297.943 7571.784Trouver le meilleur modele
env <- attr(mySequences_gr_ext_1_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"mySequences_gr_ext_1_modelTest[order(mySequences_gr_ext_1_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3587.971 7297.943 6.124032e-01 7310.634 5.273579e-01
## 84 TVM+G(4)+I 60 -3590.584 7301.169 1.220580e-01 7313.430 1.303169e-01
## 76 TIM3+G(4)+I 59 -3591.802 7301.604 9.818093e-02 7313.443 1.294385e-01
## 90 GTR+I 60 -3590.889 7301.778 9.001916e-02 7314.039 9.611019e-02
## 82 TVM+I 59 -3593.031 7304.062 2.872422e-02 7315.902 3.786906e-02
## 52 TPM3u+G(4)+I 58 -3594.204 7304.409 2.415417e-02 7315.834 3.916284e-02
## 74 TIM3+I 58 -3594.999 7305.997 1.091535e-02 7317.423 1.769783e-02
## 68 TIM2+G(4)+I 59 -3594.730 7307.461 5.250979e-03 7319.300 6.922716e-03
## 50 TPM3u+I 57 -3596.915 7307.831 4.364673e-03 7318.851 8.668272e-03
## 44 TPM2u+G(4)+I 58 -3597.244 7310.489 1.155354e-03 7321.915 1.873255e-03
## 24 TrN+G(4)+I 58 -3597.709 7311.418 7.260973e-04 7322.843 1.177272e-03
## 66 TIM2+I 58 -3597.782 7311.564 6.750246e-04 7322.989 1.094465e-03
## 60 TIM1+G(4)+I 59 -3597.020 7312.040 5.319853e-04 7323.879 7.013518e-04
## 42 TPM2u+I 57 -3599.831 7313.662 2.364295e-04 7324.682 4.695506e-04
## 16 HKY+G(4)+I 57 -3599.940 7313.879 2.120983e-04 7324.899 4.212287e-04
## 36 TPM1u+G(4)+I 58 -3599.252 7314.503 1.552180e-04 7325.929 2.516659e-04
## 22 TrN+I 57 -3600.693 7315.386 9.985248e-05 7326.406 1.983077e-04
## 58 TIM1+I 58 -3600.137 7316.274 6.402913e-05 7327.700 1.038149e-04
## 14 HKY+I 56 -3602.499 7316.999 4.457273e-05 7327.621 1.079967e-04
## 34 TPM1u+I 57 -3601.942 7317.884 2.863049e-05 7328.904 5.686036e-05
## 91 GTR+G(4) 60 -3608.088 7336.176 3.054235e-09 7348.437 3.260896e-09
## 83 TVM+G(4) 59 -3610.178 7338.357 1.026185e-09 7350.196 1.352889e-09
## 75 TIM3+G(4) 58 -3611.859 7339.717 5.198323e-10 7351.143 8.428404e-10
## 67 TIM2+G(4) 58 -3612.490 7340.980 2.764645e-10 7352.406 4.482512e-10
## 51 TPM3u+G(4) 57 -3613.728 7341.455 2.179732e-10 7352.475 4.328964e-10
## 43 TPM2u+G(4) 57 -3614.478 7342.956 1.029133e-10 7353.976 2.043865e-10
## 88 SYM+G(4)+I 58 -3614.117 7344.235 5.431292e-11 7355.660 8.806134e-11
## 23 TrN+G(4) 57 -3615.921 7345.843 2.430675e-11 7356.863 4.827337e-11
## 59 TIM1+G(4) 58 -3615.119 7346.238 1.994396e-11 7357.664 3.233653e-11
## 15 HKY+G(4) 56 -3617.671 7347.343 1.148019e-11 7357.965 2.781571e-11
## 35 TPM1u+G(4) 57 -3616.896 7347.793 9.168449e-12 7358.813 1.820860e-11
## 86 SYM+I 57 -3619.025 7352.050 1.091058e-12 7363.070 2.166849e-12
## 64 TIM2e+G(4)+I 56 -3621.474 7354.948 2.561579e-13 7365.570 6.206531e-13
## 72 TIM3e+G(4)+I 56 -3625.530 7363.060 4.436780e-15 7373.682 1.075001e-14
## 62 TIM2e+I 55 -3626.819 7363.638 3.323520e-15 7373.870 9.785204e-15
## 70 TIM3e+I 55 -3629.973 7369.946 1.418189e-16 7380.179 4.175472e-16
## 20 TrNe+G(4)+I 55 -3632.633 7375.265 9.925204e-18 7385.498 2.922208e-17
## 56 TIM1e+G(4)+I 56 -3632.112 7376.224 6.143559e-18 7386.847 1.488542e-17
## 87 SYM+G(4) 57 -3633.334 7380.668 6.661986e-19 7391.688 1.323075e-18
## 18 TrNe+I 54 -3636.827 7381.654 4.067102e-19 7391.505 1.449326e-18
## 54 TIM1e+I 55 -3636.449 7382.897 2.184939e-19 7393.130 6.432961e-19
## 63 TIM2e+G(4) 55 -3638.398 7386.796 3.110886e-20 7397.028 9.159161e-20
## 80 TVMe+G(4)+I 57 -3640.697 7395.394 4.225317e-22 7406.414 8.391509e-22
## 71 TIM3e+G(4) 55 -3645.669 7401.338 2.162868e-23 7411.571 6.367979e-23
## 78 TVMe+I 56 -3645.028 7402.056 1.510402e-23 7412.679 3.659601e-23
## 40 TPM2+G(4)+I 55 -3647.626 7405.252 3.055831e-24 7415.485 8.997066e-24
## 19 TrNe+G(4) 54 -3650.480 7408.960 4.784941e-25 7418.811 1.705130e-24
## 55 TIM1e+G(4) 55 -3649.767 7409.533 3.593143e-25 7419.766 1.057904e-24
## 48 TPM3+G(4)+I 55 -3649.949 7409.897 2.995047e-25 7420.130 8.818106e-25
## 38 TPM2+I 54 -3652.455 7412.910 6.639785e-26 7422.761 2.366111e-25
## 46 TPM3+I 54 -3653.620 7415.239 2.072258e-26 7425.090 7.384562e-26
## 79 TVMe+G(4) 56 -3652.830 7417.659 6.179642e-27 7428.281 1.497285e-26
## 12 K80+G(4)+I 54 -3656.492 7420.984 1.172001e-27 7430.835 4.176466e-27
## 28 TPM1+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 32 K81+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 39 TPM2+G(4) 54 -3657.530 7423.059 4.153240e-28 7432.910 1.480022e-27
## 10 K80+I 53 -3660.084 7426.167 8.780130e-29 7435.644 3.772061e-28
## 26 TPM1+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 30 K81+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 47 TPM3+G(4) 54 -3664.871 7437.742 2.692252e-31 7447.592 9.593935e-31
## 11 K80+G(4) 53 -3669.183 7444.365 9.812151e-33 7453.842 4.215432e-32
## 27 TPM1+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 31 K81+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 61 TIM2e 54 -3950.763 8009.526 1.856973e-155 8019.376 6.617388e-155
## 85 SYM 56 -3949.430 8010.860 9.528525e-156 8021.482 2.308696e-155
## 65 TIM2 57 -3951.784 8017.568 3.330033e-157 8028.588 6.613469e-157
## 89 GTR 59 -3950.578 8019.156 1.504917e-157 8030.996 1.984033e-157
## 41 TPM2u 56 -3959.441 8030.882 4.277783e-160 8041.505 1.036477e-159
## 81 TVM 58 -3958.200 8032.401 2.002303e-160 8043.826 3.246473e-160
## 21 TrN 56 -3973.238 8058.476 4.358826e-166 8069.098 1.056114e-165
## 73 TIM3 57 -3973.069 8060.138 1.898376e-166 8071.158 3.770188e-166
## 57 TIM1 57 -3973.229 8060.459 1.617371e-166 8071.479 3.212110e-166
## 37 TPM2 53 -3978.025 8062.049 7.302601e-167 8071.526 3.137295e-166
## 77 TVMe 55 -3976.644 8063.287 3.931877e-167 8073.520 1.157635e-166
## 17 TrNe 53 -3982.480 8070.961 8.478992e-169 8080.438 3.642689e-168
## 13 HKY 55 -3980.945 8071.890 5.326671e-169 8082.123 1.568294e-168
## 69 TIM3e 54 -3982.132 8072.264 4.419060e-169 8082.115 1.574747e-168
## 53 TIM1e 54 -3982.480 8072.960 3.120240e-169 8082.811 1.111908e-168
## 49 TPM3u 56 -3980.797 8073.594 2.272693e-169 8084.216 5.506578e-169
## 33 TPM1u 56 -3980.936 8073.872 1.977647e-169 8084.494 4.791704e-169
## 9 K80 52 -4009.619 8123.239 3.769941e-180 8132.349 1.944935e-179
## 45 TPM3 53 -4009.324 8124.648 1.863147e-180 8134.125 8.004330e-180
## 25 TPM1 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 29 K81 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 8 F81+G(4)+I 56 -4014.507 8141.014 5.204601e-184 8151.637 1.261039e-183
## 6 F81+I 55 -4017.012 8144.023 1.156244e-184 8154.256 3.404248e-184
## 7 F81+G(4) 55 -4024.227 8158.455 8.496664e-188 8168.687 2.501613e-187
## 4 JC+G(4)+I 53 -4058.196 8222.392 1.110371e-201 8231.869 4.770304e-201
## 2 JC+I 52 -4059.860 8223.720 5.716742e-202 8232.830 2.949301e-201
## 3 JC+G(4) 52 -4068.427 8240.854 1.087487e-205 8249.965 5.610409e-205
## 5 F81 54 -4314.488 8736.975 2.018815e-313 8746.826 7.194117e-313
## 1 JC 51 -4344.147 8790.293 0.000000e+00 8799.046 4.940656e-324
## BIC
## 92 7571.784
## 84 7570.521
## 76 7566.467
## 90 7571.130
## 82 7568.925
## 52 7564.783
## 74 7566.371
## 68 7572.324
## 50 7563.715
## 44 7570.863
## 24 7571.792
## 66 7571.938
## 60 7576.903
## 42 7569.547
## 16 7569.764
## 36 7574.877
## 22 7571.270
## 58 7576.648
## 14 7568.394
## 34 7573.769
## 91 7605.528
## 83 7603.220
## 75 7600.091
## 67 7601.354
## 51 7597.340
## 43 7598.841
## 88 7604.609
## 23 7601.727
## 59 7606.612
## 15 7598.738
## 35 7603.677
## 86 7607.935
## 64 7606.344
## 72 7614.455
## 62 7610.544
## 70 7616.852
## 20 7622.171
## 56 7627.620
## 87 7636.552
## 18 7624.072
## 54 7629.803
## 63 7633.702
## 80 7651.278
## 71 7648.244
## 78 7653.452
## 40 7652.158
## 19 7651.377
## 55 7656.440
## 48 7656.804
## 38 7655.327
## 46 7657.656
## 79 7669.055
## 12 7663.401
## 28 7668.845
## 32 7668.845
## 39 7665.476
## 10 7664.095
## 26 7669.859
## 30 7669.859
## 47 7680.159
## 11 7682.293
## 27 7687.595
## 31 7687.595
## 61 8251.943
## 85 8262.256
## 65 8273.453
## 89 8284.019
## 41 8282.278
## 81 8292.775
## 21 8309.871
## 73 8316.023
## 57 8316.343
## 37 8299.977
## 77 8310.194
## 17 8308.889
## 13 8318.797
## 69 8314.681
## 53 8315.377
## 49 8324.989
## 33 8325.268
## 9 8356.677
## 45 8362.576
## 25 8363.166
## 29 8363.166
## 8 8392.410
## 6 8390.929
## 7 8405.361
## 4 8460.320
## 2 8457.158
## 3 8474.293
## 5 8979.392
## 1 9019.243mySequences_gr_ext_1_modelTest[order(mySequences_gr_ext_1_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 50 TPM3u+I 57 -3596.915 7307.831 4.364673e-03 7318.851 8.668272e-03
## 52 TPM3u+G(4)+I 58 -3594.204 7304.409 2.415417e-02 7315.834 3.916284e-02
## 74 TIM3+I 58 -3594.999 7305.997 1.091535e-02 7317.423 1.769783e-02
## 76 TIM3+G(4)+I 59 -3591.802 7301.604 9.818093e-02 7313.443 1.294385e-01
## 14 HKY+I 56 -3602.499 7316.999 4.457273e-05 7327.621 1.079967e-04
## 82 TVM+I 59 -3593.031 7304.062 2.872422e-02 7315.902 3.786906e-02
## 42 TPM2u+I 57 -3599.831 7313.662 2.364295e-04 7324.682 4.695506e-04
## 16 HKY+G(4)+I 57 -3599.940 7313.879 2.120983e-04 7324.899 4.212287e-04
## 84 TVM+G(4)+I 60 -3590.584 7301.169 1.220580e-01 7313.430 1.303169e-01
## 44 TPM2u+G(4)+I 58 -3597.244 7310.489 1.155354e-03 7321.915 1.873255e-03
## 90 GTR+I 60 -3590.889 7301.778 9.001916e-02 7314.039 9.611019e-02
## 22 TrN+I 57 -3600.693 7315.386 9.985248e-05 7326.406 1.983077e-04
## 92 GTR+G(4)+I 61 -3587.971 7297.943 6.124032e-01 7310.634 5.273579e-01
## 24 TrN+G(4)+I 58 -3597.709 7311.418 7.260973e-04 7322.843 1.177272e-03
## 66 TIM2+I 58 -3597.782 7311.564 6.750246e-04 7322.989 1.094465e-03
## 68 TIM2+G(4)+I 59 -3594.730 7307.461 5.250979e-03 7319.300 6.922716e-03
## 34 TPM1u+I 57 -3601.942 7317.884 2.863049e-05 7328.904 5.686036e-05
## 36 TPM1u+G(4)+I 58 -3599.252 7314.503 1.552180e-04 7325.929 2.516659e-04
## 58 TIM1+I 58 -3600.137 7316.274 6.402913e-05 7327.700 1.038149e-04
## 60 TIM1+G(4)+I 59 -3597.020 7312.040 5.319853e-04 7323.879 7.013518e-04
## 51 TPM3u+G(4) 57 -3613.728 7341.455 2.179732e-10 7352.475 4.328964e-10
## 15 HKY+G(4) 56 -3617.671 7347.343 1.148019e-11 7357.965 2.781571e-11
## 43 TPM2u+G(4) 57 -3614.478 7342.956 1.029133e-10 7353.976 2.043865e-10
## 75 TIM3+G(4) 58 -3611.859 7339.717 5.198323e-10 7351.143 8.428404e-10
## 67 TIM2+G(4) 58 -3612.490 7340.980 2.764645e-10 7352.406 4.482512e-10
## 23 TrN+G(4) 57 -3615.921 7345.843 2.430675e-11 7356.863 4.827337e-11
## 83 TVM+G(4) 59 -3610.178 7338.357 1.026185e-09 7350.196 1.352889e-09
## 35 TPM1u+G(4) 57 -3616.896 7347.793 9.168449e-12 7358.813 1.820860e-11
## 88 SYM+G(4)+I 58 -3614.117 7344.235 5.431292e-11 7355.660 8.806134e-11
## 91 GTR+G(4) 60 -3608.088 7336.176 3.054235e-09 7348.437 3.260896e-09
## 64 TIM2e+G(4)+I 56 -3621.474 7354.948 2.561579e-13 7365.570 6.206531e-13
## 59 TIM1+G(4) 58 -3615.119 7346.238 1.994396e-11 7357.664 3.233653e-11
## 86 SYM+I 57 -3619.025 7352.050 1.091058e-12 7363.070 2.166849e-12
## 62 TIM2e+I 55 -3626.819 7363.638 3.323520e-15 7373.870 9.785204e-15
## 72 TIM3e+G(4)+I 56 -3625.530 7363.060 4.436780e-15 7373.682 1.075001e-14
## 70 TIM3e+I 55 -3629.973 7369.946 1.418189e-16 7380.179 4.175472e-16
## 20 TrNe+G(4)+I 55 -3632.633 7375.265 9.925204e-18 7385.498 2.922208e-17
## 18 TrNe+I 54 -3636.827 7381.654 4.067102e-19 7391.505 1.449326e-18
## 56 TIM1e+G(4)+I 56 -3632.112 7376.224 6.143559e-18 7386.847 1.488542e-17
## 54 TIM1e+I 55 -3636.449 7382.897 2.184939e-19 7393.130 6.432961e-19
## 63 TIM2e+G(4) 55 -3638.398 7386.796 3.110886e-20 7397.028 9.159161e-20
## 87 SYM+G(4) 57 -3633.334 7380.668 6.661986e-19 7391.688 1.323075e-18
## 71 TIM3e+G(4) 55 -3645.669 7401.338 2.162868e-23 7411.571 6.367979e-23
## 80 TVMe+G(4)+I 57 -3640.697 7395.394 4.225317e-22 7406.414 8.391509e-22
## 19 TrNe+G(4) 54 -3650.480 7408.960 4.784941e-25 7418.811 1.705130e-24
## 40 TPM2+G(4)+I 55 -3647.626 7405.252 3.055831e-24 7415.485 8.997066e-24
## 78 TVMe+I 56 -3645.028 7402.056 1.510402e-23 7412.679 3.659601e-23
## 38 TPM2+I 54 -3652.455 7412.910 6.639785e-26 7422.761 2.366111e-25
## 55 TIM1e+G(4) 55 -3649.767 7409.533 3.593143e-25 7419.766 1.057904e-24
## 48 TPM3+G(4)+I 55 -3649.949 7409.897 2.995047e-25 7420.130 8.818106e-25
## 46 TPM3+I 54 -3653.620 7415.239 2.072258e-26 7425.090 7.384562e-26
## 12 K80+G(4)+I 54 -3656.492 7420.984 1.172001e-27 7430.835 4.176466e-27
## 10 K80+I 53 -3660.084 7426.167 8.780130e-29 7435.644 3.772061e-28
## 39 TPM2+G(4) 54 -3657.530 7423.059 4.153240e-28 7432.910 1.480022e-27
## 28 TPM1+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 32 K81+G(4)+I 55 -3655.970 7421.939 7.270917e-28 7432.172 2.140725e-27
## 79 TVMe+G(4) 56 -3652.830 7417.659 6.179642e-27 7428.281 1.497285e-26
## 26 TPM1+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 30 K81+I 54 -3659.721 7427.442 4.642004e-29 7437.292 1.654194e-28
## 47 TPM3+G(4) 54 -3664.871 7437.742 2.692252e-31 7447.592 9.593935e-31
## 11 K80+G(4) 53 -3669.183 7444.365 9.812151e-33 7453.842 4.215432e-32
## 27 TPM1+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 31 K81+G(4) 54 -3668.589 7445.178 6.536117e-33 7455.029 2.329168e-32
## 61 TIM2e 54 -3950.763 8009.526 1.856973e-155 8019.376 6.617388e-155
## 85 SYM 56 -3949.430 8010.860 9.528525e-156 8021.482 2.308696e-155
## 65 TIM2 57 -3951.784 8017.568 3.330033e-157 8028.588 6.613469e-157
## 41 TPM2u 56 -3959.441 8030.882 4.277783e-160 8041.505 1.036477e-159
## 89 GTR 59 -3950.578 8019.156 1.504917e-157 8030.996 1.984033e-157
## 81 TVM 58 -3958.200 8032.401 2.002303e-160 8043.826 3.246473e-160
## 37 TPM2 53 -3978.025 8062.049 7.302601e-167 8071.526 3.137295e-166
## 17 TrNe 53 -3982.480 8070.961 8.478992e-169 8080.438 3.642689e-168
## 21 TrN 56 -3973.238 8058.476 4.358826e-166 8069.098 1.056114e-165
## 77 TVMe 55 -3976.644 8063.287 3.931877e-167 8073.520 1.157635e-166
## 69 TIM3e 54 -3982.132 8072.264 4.419060e-169 8082.115 1.574747e-168
## 53 TIM1e 54 -3982.480 8072.960 3.120240e-169 8082.811 1.111908e-168
## 73 TIM3 57 -3973.069 8060.138 1.898376e-166 8071.158 3.770188e-166
## 57 TIM1 57 -3973.229 8060.459 1.617371e-166 8071.479 3.212110e-166
## 13 HKY 55 -3980.945 8071.890 5.326671e-169 8082.123 1.568294e-168
## 49 TPM3u 56 -3980.797 8073.594 2.272693e-169 8084.216 5.506578e-169
## 33 TPM1u 56 -3980.936 8073.872 1.977647e-169 8084.494 4.791704e-169
## 9 K80 52 -4009.619 8123.239 3.769941e-180 8132.349 1.944935e-179
## 45 TPM3 53 -4009.324 8124.648 1.863147e-180 8134.125 8.004330e-180
## 25 TPM1 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 29 K81 53 -4009.619 8125.238 1.387334e-180 8134.715 5.960172e-180
## 6 F81+I 55 -4017.012 8144.023 1.156244e-184 8154.256 3.404248e-184
## 8 F81+G(4)+I 56 -4014.507 8141.014 5.204601e-184 8151.637 1.261039e-183
## 7 F81+G(4) 55 -4024.227 8158.455 8.496664e-188 8168.687 2.501613e-187
## 2 JC+I 52 -4059.860 8223.720 5.716742e-202 8232.830 2.949301e-201
## 4 JC+G(4)+I 53 -4058.196 8222.392 1.110371e-201 8231.869 4.770304e-201
## 3 JC+G(4) 52 -4068.427 8240.854 1.087487e-205 8249.965 5.610409e-205
## 5 F81 54 -4314.488 8736.975 2.018815e-313 8746.826 7.194117e-313
## 1 JC 51 -4344.147 8790.293 0.000000e+00 8799.046 4.940656e-324
## BIC
## 50 7563.715
## 52 7564.783
## 74 7566.371
## 76 7566.467
## 14 7568.394
## 82 7568.925
## 42 7569.547
## 16 7569.764
## 84 7570.521
## 44 7570.863
## 90 7571.130
## 22 7571.270
## 92 7571.784
## 24 7571.792
## 66 7571.938
## 68 7572.324
## 34 7573.769
## 36 7574.877
## 58 7576.648
## 60 7576.903
## 51 7597.340
## 15 7598.738
## 43 7598.841
## 75 7600.091
## 67 7601.354
## 23 7601.727
## 83 7603.220
## 35 7603.677
## 88 7604.609
## 91 7605.528
## 64 7606.344
## 59 7606.612
## 86 7607.935
## 62 7610.544
## 72 7614.455
## 70 7616.852
## 20 7622.171
## 18 7624.072
## 56 7627.620
## 54 7629.803
## 63 7633.702
## 87 7636.552
## 71 7648.244
## 80 7651.278
## 19 7651.377
## 40 7652.158
## 78 7653.452
## 38 7655.327
## 55 7656.440
## 48 7656.804
## 46 7657.656
## 12 7663.401
## 10 7664.095
## 39 7665.476
## 28 7668.845
## 32 7668.845
## 79 7669.055
## 26 7669.859
## 30 7669.859
## 47 7680.159
## 11 7682.293
## 27 7687.595
## 31 7687.595
## 61 8251.943
## 85 8262.256
## 65 8273.453
## 41 8282.278
## 89 8284.019
## 81 8292.775
## 37 8299.977
## 17 8308.889
## 21 8309.871
## 77 8310.194
## 69 8314.681
## 53 8315.377
## 73 8316.023
## 57 8316.343
## 13 8318.797
## 49 8324.989
## 33 8325.268
## 9 8356.677
## 45 8362.576
## 25 8363.166
## 29 8363.166
## 6 8390.929
## 8 8392.410
## 7 8405.361
## 2 8457.158
## 4 8460.320
## 3 8474.293
## 5 8979.392
## 1 9019.243Meilleur modele: TIM3+G(4)+I
env$`TIM3+G(4)+I`## pml(tree = `tree_TIM3+G(4)+I`, data = data, bf = c(0.267772915837927,
## 0.26993237483662, 0.170199465818037, 0.292095243507416), Q = c(0.216488832975341,
## 10.4697492964762, 1, 0.216488832975341, 14.0840108381235, 1),
## model = "TIM3", inv = 0.600116676053066, k = 4, shape = 5.33821822461735)Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_1 = dist.dna(mySequences_align_gr_ext_1_ape, pairwise.deletion=FALSE, model="TN93") # TIM3 existe pas donc utilise un modele similaire
# Construction arbre NJ
treeNJ_gr_ext_1 <- NJ(mySequences_align_gr_ext_1)
# Visualisation
plot(treeNJ_gr_ext_1, main="Arbre NJ Groupe externe 1")
Integration des parametres
fit_gr_ext_1 = pml(treeNJ_gr_ext_1, data=mySequences_align_gr_ext_1_phangorn)
fitTIM3_gr_ext_1 <- update(fit_gr_ext_1, model="TIM3", k=4, inv=0.600116108726824, shape=5.33769016071792)
fitTIM3_gr_ext_1 <- optim.pml(fitTIM3_gr_ext_1, model="TIM3", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_gr_ext_1 = bootstrap.pml(fitTIM3_gr_ext_1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM3_gr_ext_1$tree), bs_gr_ext_1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
AA
Alignement
mySequences_align_aa_gr_ext_1 = AlignTranslation(Sequences_groupe_externe_1,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.04 secs
##
## Alignment converged - skipping remaining iteration.Conversion
mySequences_align_aa_gr_ext_1_ape = as.AAbin(mySequences_align_aa_gr_ext_1)
mySequences_align_aa_gr_ext_1_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_1_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Recherche du meilleur modele
mySequences_align_aa_gr_ext_1_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_1_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 51 -788.1395 1678.279 1850.182
## WAG+I 52 -780.0185 1664.037 1839.31
## WAG+G(4) 52 -780.9756 1665.951 1841.224
## WAG+G(4)+I 53 -780.1385 1666.277 1844.921
## JTT 51 -785.7615 1673.523 1845.426
## JTT+I 52 -777.8272 1659.654 1834.928
## JTT+G(4) 52 -778.7116 1661.423 1836.696
## JTT+G(4)+I 53 -777.9091 1661.818 1840.462
## LG 51 -784.6328 1671.266 1843.168
## LG+I 52 -777.2918 1658.584 1833.857
## LG+G(4) 52 -777.9279 1659.856 1835.129
## LG+G(4)+I 53 -777.3025 1660.605 1839.249
## Dayhoff 51 -798.247 1698.494 1870.397
## Dayhoff+I 52 -789.6021 1683.204 1858.477
## Dayhoff+G(4) 52 -790.7679 1685.536 1860.809
## Dayhoff+G(4)+I 53 -789.7597 1685.519 1864.163
## cpREV 51 -776.6083 1655.217 1827.119
## cpREV+I 52 -768.4012 1640.802 1816.076
## cpREV+G(4) 52 -769.3804 1642.761 1818.034
## cpREV+G(4)+I 53 -768.412 1642.824 1821.468
## mtmam 51 -749.5626 1601.125 1773.028
## mtmam+I 52 -743.835 1591.67 1766.943
## mtmam+G(4) 52 -743.9617 1591.923 1767.197
## mtmam+G(4)+I 53 -743.8491 1593.698 1772.342
## mtArt 51 -751.6583 1605.317 1777.219
## mtArt+I 52 -745.7645 1595.529 1770.802
## mtArt+G(4) 52 -745.9259 1595.852 1771.125
## mtArt+G(4)+I 53 -745.7749 1597.55 1776.194
## MtZoa 51 -745.6115 1593.223 1765.125
## MtZoa+I 52 -739.7715 1583.543 1758.816
## MtZoa+G(4) 52 -739.9347 1583.869 1759.143
## MtZoa+G(4)+I 53 -739.7824 1585.565 1764.209
## mtREV24 51 -753.1828 1608.366 1780.268
## mtREV24+I 52 -746.7021 1597.404 1772.677
## mtREV24+G(4) 52 -746.9918 1597.984 1773.257
## mtREV24+G(4)+I 53 -746.8171 1599.634 1778.278
## VT 51 -779.4572 1660.914 1832.817
## VT+I 52 -772.429 1648.858 1824.131
## VT+G(4) 52 -772.932 1649.864 1825.137
## VT+G(4)+I 53 -772.4382 1650.876 1829.52
## RtREV 51 -788.3544 1678.709 1850.611
## RtREV+I 52 -781.0579 1666.116 1841.389
## RtREV+G(4) 52 -781.6547 1667.309 1842.583
## RtREV+G(4)+I 53 -781.066 1668.132 1846.776
## HIVw 51 -818.7671 1739.534 1911.437
## HIVw+I 52 -808.7011 1721.402 1896.675
## HIVw+G(4) 52 -810.1672 1724.334 1899.608
## HIVw+G(4)+I 53 -808.8783 1723.757 1902.4
## HIVb 51 -797.2001 1696.4 1868.303
## HIVb+I 52 -789.0109 1682.022 1857.295
## HIVb+G(4) 52 -789.9841 1683.968 1859.241
## HIVb+G(4)+I 53 -789.1577 1684.315 1862.959
## FLU 51 -794.6883 1691.377 1863.279
## FLU+I 52 -787.7828 1679.566 1854.839
## FLU+G(4) 52 -788.253 1680.506 1855.779
## FLU+G(4)+I 53 -787.8793 1681.759 1860.402
## Blosum62 51 -784.1843 1670.369 1842.271
## Blosum62+I 52 -776.8406 1657.681 1832.954
## Blosum62+G(4) 52 -777.4875 1658.975 1834.248
## Blosum62+G(4)+I 53 -776.8913 1659.783 1838.426
## Dayhoff_DCMut 51 -798.2997 1698.599 1870.502
## Dayhoff_DCMut+I 52 -789.6592 1683.318 1858.592
## Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 1860.921
## Dayhoff_DCMut+G(4)+I 53 -789.817 1685.634 1864.278
## JTT_DCMut 51 -786.2536 1674.507 1846.41
## JTT_DCMut+I 52 -778.2773 1660.555 1835.828
## JTT_DCMut+G(4) 52 -779.1775 1662.355 1837.628
## JTT_DCMut+G(4)+I 53 -778.3787 1662.757 1841.401Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_1_modeltest, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"mySequences_align_aa_gr_ext_1_modeltest[order(mySequences_align_aa_gr_ext_1_modeltest$AIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -739.7715 1583.543 4.410271e-01 1617.568
## 31 MtZoa+G(4) 52 -739.9347 1583.869 3.745911e-01 1617.894
## 32 MtZoa+G(4)+I 53 -739.7824 1585.565 1.604755e-01 1621.118
## 22 mtmam+I 52 -743.8350 1591.670 7.580609e-03 1625.695
## 23 mtmam+G(4) 52 -743.9617 1591.923 6.678514e-03 1625.948
## 29 MtZoa 51 -745.6115 1593.223 3.487145e-03 1625.763
## 24 mtmam+G(4)+I 53 -743.8491 1593.698 2.749564e-03 1629.251
## 26 mtArt+I 52 -745.7645 1595.529 1.100847e-03 1629.554
## 27 mtArt+G(4) 52 -745.9259 1595.852 9.367109e-04 1629.877
## 34 mtREV24+I 52 -746.7021 1597.404 4.310365e-04 1631.429
## 28 mtArt+G(4)+I 53 -745.7749 1597.550 4.007711e-04 1633.103
## 35 mtREV24+G(4) 52 -746.9918 1597.984 3.226418e-04 1632.008
## 36 mtREV24+G(4)+I 53 -746.8171 1599.634 1.413471e-04 1635.187
## 21 mtmam 51 -749.5626 1601.125 6.707159e-05 1633.665
## 25 mtArt 51 -751.6583 1605.317 8.248022e-06 1637.857
## 33 mtREV24 51 -753.1828 1608.366 1.795847e-06 1640.906
## 18 cpREV+I 52 -768.4012 1640.802 1.624453e-13 1674.827
## 19 cpREV+G(4) 52 -769.3804 1642.761 6.102067e-14 1676.785
## 20 cpREV+G(4)+I 53 -768.4120 1642.824 5.912208e-14 1678.377
## 38 VT+I 52 -772.4290 1648.858 2.893890e-15 1682.883
## 39 VT+G(4) 52 -772.9320 1649.864 1.749909e-15 1683.889
## 40 VT+G(4)+I 53 -772.4382 1650.876 1.054842e-15 1686.429
## 17 cpREV 51 -776.6083 1655.217 1.204272e-16 1687.756
## 58 Blosum62+I 52 -776.8406 1657.681 3.511969e-17 1691.706
## 10 LG+I 52 -777.2918 1658.584 2.236507e-17 1692.608
## 59 Blosum62+G(4) 52 -777.4875 1658.975 1.839098e-17 1693.000
## 6 JTT+I 52 -777.8272 1659.654 1.309358e-17 1693.679
## 60 Blosum62+G(4)+I 53 -776.8913 1659.783 1.228126e-17 1695.335
## 11 LG+G(4) 52 -777.9279 1659.856 1.183988e-17 1693.880
## 66 JTT_DCMut+I 52 -778.2773 1660.555 8.348192e-18 1694.579
## 12 LG+G(4)+I 53 -777.3025 1660.605 8.140374e-18 1696.158
## 37 VT 51 -779.4572 1660.914 6.973852e-18 1693.454
## 7 JTT+G(4) 52 -778.7116 1661.423 5.407067e-18 1695.448
## 8 JTT+G(4)+I 53 -777.9091 1661.818 4.438293e-18 1697.371
## 67 JTT_DCMut+G(4) 52 -779.1775 1662.355 3.393520e-18 1696.380
## 68 JTT_DCMut+G(4)+I 53 -778.3787 1662.757 2.775001e-18 1698.310
## 2 WAG+I 52 -780.0185 1664.037 1.463465e-18 1698.062
## 3 WAG+G(4) 52 -780.9756 1665.951 5.620186e-19 1699.976
## 42 RtREV+I 52 -781.0579 1666.116 5.175693e-19 1700.141
## 4 WAG+G(4)+I 53 -780.1385 1666.277 4.775312e-19 1701.830
## 43 RtREV+G(4) 52 -781.6547 1667.309 2.849806e-19 1701.334
## 44 RtREV+G(4)+I 53 -781.0660 1668.132 1.888820e-19 1703.685
## 57 Blosum62 51 -784.1843 1670.369 6.173369e-20 1702.908
## 9 LG 51 -784.6328 1671.266 3.941927e-20 1703.806
## 5 JTT 51 -785.7615 1673.523 1.275021e-20 1706.063
## 65 JTT_DCMut 51 -786.2536 1674.507 7.795348e-21 1707.047
## 1 WAG 51 -788.1395 1678.279 1.182432e-21 1710.819
## 41 RtREV 51 -788.3544 1678.709 9.537921e-22 1711.249
## 54 FLU+I 52 -787.7828 1679.566 6.214320e-22 1713.590
## 55 FLU+G(4) 52 -788.2530 1680.506 3.883167e-22 1714.531
## 56 FLU+G(4)+I 53 -787.8793 1681.759 2.075831e-22 1717.311
## 50 HIVb+I 52 -789.0109 1682.022 1.819948e-22 1716.046
## 14 Dayhoff+I 52 -789.6021 1683.204 1.007611e-22 1717.229
## 62 Dayhoff_DCMut+I 52 -789.6592 1683.318 9.516454e-23 1717.343
## 51 HIVb+G(4) 52 -789.9841 1683.968 6.876835e-23 1717.993
## 52 HIVb+G(4)+I 53 -789.1577 1684.315 5.780657e-23 1719.868
## 16 Dayhoff+G(4)+I 53 -789.7597 1685.519 3.166325e-23 1721.072
## 15 Dayhoff+G(4) 52 -790.7679 1685.536 3.140474e-23 1719.560
## 64 Dayhoff_DCMut+G(4)+I 53 -789.8170 1685.634 2.989975e-23 1721.187
## 63 Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 2.969622e-23 1719.672
## 53 FLU 51 -794.6883 1691.377 1.693148e-24 1723.916
## 49 HIVb 51 -797.2001 1696.400 1.373472e-25 1728.940
## 13 Dayhoff 51 -798.2470 1698.494 4.821127e-26 1731.034
## 61 Dayhoff_DCMut 51 -798.2997 1698.599 4.573673e-26 1731.139
## 46 HIVw+I 52 -808.7011 1721.402 5.113132e-31 1755.427
## 48 HIVw+G(4)+I 53 -808.8783 1723.757 1.575570e-31 1759.309
## 47 HIVw+G(4) 52 -810.1672 1724.334 1.180213e-31 1758.359
## 45 HIVw 51 -818.7671 1739.534 5.907050e-35 1772.074
## AICcw BIC
## 30 4.812417e-01 1758.816
## 31 4.087478e-01 1759.143
## 32 8.156114e-02 1764.209
## 22 8.271839e-03 1766.943
## 23 7.287488e-03 1767.197
## 29 7.994499e-03 1765.125
## 24 1.397457e-03 1772.342
## 26 1.201227e-03 1770.802
## 27 1.022124e-03 1771.125
## 34 4.703401e-04 1772.677
## 28 2.036905e-04 1776.194
## 35 3.520616e-04 1773.257
## 36 7.183917e-05 1778.278
## 21 1.537658e-04 1773.028
## 25 1.890911e-05 1777.219
## 33 4.117093e-06 1780.268
## 18 1.772577e-13 1816.076
## 19 6.658478e-14 1818.034
## 20 3.004860e-14 1821.468
## 38 3.157767e-15 1824.131
## 39 1.909473e-15 1825.137
## 40 5.361198e-16 1829.520
## 17 2.760869e-16 1827.119
## 58 3.832204e-17 1832.954
## 10 2.440441e-17 1833.857
## 59 2.006795e-17 1834.248
## 6 1.428751e-17 1834.928
## 60 6.241906e-18 1838.426
## 11 1.291949e-17 1835.129
## 66 9.109414e-18 1835.828
## 12 4.137318e-18 1839.249
## 37 1.598799e-17 1832.817
## 7 5.900105e-18 1836.696
## 8 2.255748e-18 1840.462
## 67 3.702955e-18 1837.628
## 68 1.410385e-18 1841.401
## 2 1.596910e-18 1839.310
## 3 6.132657e-19 1841.224
## 42 5.647633e-19 1841.389
## 4 2.427036e-19 1844.921
## 43 3.109663e-19 1842.583
## 44 9.599864e-20 1846.776
## 57 1.415284e-19 1842.271
## 9 9.037116e-20 1843.168
## 5 2.923065e-20 1845.426
## 65 1.787133e-20 1846.410
## 1 2.710800e-21 1850.182
## 41 2.186628e-21 1850.611
## 54 6.780967e-22 1854.839
## 55 4.237250e-22 1855.779
## 56 1.055034e-22 1860.402
## 50 1.985898e-22 1857.295
## 14 1.099490e-22 1858.477
## 62 1.038420e-22 1858.592
## 51 7.503892e-23 1859.241
## 52 2.938000e-23 1862.959
## 16 1.609274e-23 1864.163
## 15 3.426835e-23 1860.809
## 64 1.519645e-23 1864.278
## 63 3.240404e-23 1860.921
## 53 3.881649e-24 1863.279
## 49 3.148771e-25 1868.303
## 13 1.105274e-25 1870.397
## 61 1.048543e-25 1870.502
## 46 5.579368e-31 1896.675
## 48 8.007783e-32 1902.400
## 47 1.287830e-31 1899.608
## 45 1.354228e-34 1911.437mySequences_align_aa_gr_ext_1_modeltest[order(mySequences_align_aa_gr_ext_1_modeltest$BIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -739.7715 1583.543 4.410271e-01 1617.568
## 31 MtZoa+G(4) 52 -739.9347 1583.869 3.745911e-01 1617.894
## 32 MtZoa+G(4)+I 53 -739.7824 1585.565 1.604755e-01 1621.118
## 29 MtZoa 51 -745.6115 1593.223 3.487145e-03 1625.763
## 22 mtmam+I 52 -743.8350 1591.670 7.580609e-03 1625.695
## 23 mtmam+G(4) 52 -743.9617 1591.923 6.678514e-03 1625.948
## 26 mtArt+I 52 -745.7645 1595.529 1.100847e-03 1629.554
## 27 mtArt+G(4) 52 -745.9259 1595.852 9.367109e-04 1629.877
## 24 mtmam+G(4)+I 53 -743.8491 1593.698 2.749564e-03 1629.251
## 34 mtREV24+I 52 -746.7021 1597.404 4.310365e-04 1631.429
## 21 mtmam 51 -749.5626 1601.125 6.707159e-05 1633.665
## 35 mtREV24+G(4) 52 -746.9918 1597.984 3.226418e-04 1632.008
## 28 mtArt+G(4)+I 53 -745.7749 1597.550 4.007711e-04 1633.103
## 25 mtArt 51 -751.6583 1605.317 8.248022e-06 1637.857
## 36 mtREV24+G(4)+I 53 -746.8171 1599.634 1.413471e-04 1635.187
## 33 mtREV24 51 -753.1828 1608.366 1.795847e-06 1640.906
## 18 cpREV+I 52 -768.4012 1640.802 1.624453e-13 1674.827
## 19 cpREV+G(4) 52 -769.3804 1642.761 6.102067e-14 1676.785
## 20 cpREV+G(4)+I 53 -768.4120 1642.824 5.912208e-14 1678.377
## 38 VT+I 52 -772.4290 1648.858 2.893890e-15 1682.883
## 39 VT+G(4) 52 -772.9320 1649.864 1.749909e-15 1683.889
## 17 cpREV 51 -776.6083 1655.217 1.204272e-16 1687.756
## 40 VT+G(4)+I 53 -772.4382 1650.876 1.054842e-15 1686.429
## 37 VT 51 -779.4572 1660.914 6.973852e-18 1693.454
## 58 Blosum62+I 52 -776.8406 1657.681 3.511969e-17 1691.706
## 10 LG+I 52 -777.2918 1658.584 2.236507e-17 1692.608
## 59 Blosum62+G(4) 52 -777.4875 1658.975 1.839098e-17 1693.000
## 6 JTT+I 52 -777.8272 1659.654 1.309358e-17 1693.679
## 11 LG+G(4) 52 -777.9279 1659.856 1.183988e-17 1693.880
## 66 JTT_DCMut+I 52 -778.2773 1660.555 8.348192e-18 1694.579
## 7 JTT+G(4) 52 -778.7116 1661.423 5.407067e-18 1695.448
## 67 JTT_DCMut+G(4) 52 -779.1775 1662.355 3.393520e-18 1696.380
## 60 Blosum62+G(4)+I 53 -776.8913 1659.783 1.228126e-17 1695.335
## 12 LG+G(4)+I 53 -777.3025 1660.605 8.140374e-18 1696.158
## 2 WAG+I 52 -780.0185 1664.037 1.463465e-18 1698.062
## 8 JTT+G(4)+I 53 -777.9091 1661.818 4.438293e-18 1697.371
## 3 WAG+G(4) 52 -780.9756 1665.951 5.620186e-19 1699.976
## 42 RtREV+I 52 -781.0579 1666.116 5.175693e-19 1700.141
## 68 JTT_DCMut+G(4)+I 53 -778.3787 1662.757 2.775001e-18 1698.310
## 57 Blosum62 51 -784.1843 1670.369 6.173369e-20 1702.908
## 43 RtREV+G(4) 52 -781.6547 1667.309 2.849806e-19 1701.334
## 9 LG 51 -784.6328 1671.266 3.941927e-20 1703.806
## 4 WAG+G(4)+I 53 -780.1385 1666.277 4.775312e-19 1701.830
## 5 JTT 51 -785.7615 1673.523 1.275021e-20 1706.063
## 65 JTT_DCMut 51 -786.2536 1674.507 7.795348e-21 1707.047
## 44 RtREV+G(4)+I 53 -781.0660 1668.132 1.888820e-19 1703.685
## 1 WAG 51 -788.1395 1678.279 1.182432e-21 1710.819
## 41 RtREV 51 -788.3544 1678.709 9.537921e-22 1711.249
## 54 FLU+I 52 -787.7828 1679.566 6.214320e-22 1713.590
## 55 FLU+G(4) 52 -788.2530 1680.506 3.883167e-22 1714.531
## 50 HIVb+I 52 -789.0109 1682.022 1.819948e-22 1716.046
## 14 Dayhoff+I 52 -789.6021 1683.204 1.007611e-22 1717.229
## 62 Dayhoff_DCMut+I 52 -789.6592 1683.318 9.516454e-23 1717.343
## 51 HIVb+G(4) 52 -789.9841 1683.968 6.876835e-23 1717.993
## 56 FLU+G(4)+I 53 -787.8793 1681.759 2.075831e-22 1717.311
## 15 Dayhoff+G(4) 52 -790.7679 1685.536 3.140474e-23 1719.560
## 63 Dayhoff_DCMut+G(4) 52 -790.8238 1685.648 2.969622e-23 1719.672
## 52 HIVb+G(4)+I 53 -789.1577 1684.315 5.780657e-23 1719.868
## 53 FLU 51 -794.6883 1691.377 1.693148e-24 1723.916
## 16 Dayhoff+G(4)+I 53 -789.7597 1685.519 3.166325e-23 1721.072
## 64 Dayhoff_DCMut+G(4)+I 53 -789.8170 1685.634 2.989975e-23 1721.187
## 49 HIVb 51 -797.2001 1696.400 1.373472e-25 1728.940
## 13 Dayhoff 51 -798.2470 1698.494 4.821127e-26 1731.034
## 61 Dayhoff_DCMut 51 -798.2997 1698.599 4.573673e-26 1731.139
## 46 HIVw+I 52 -808.7011 1721.402 5.113132e-31 1755.427
## 47 HIVw+G(4) 52 -810.1672 1724.334 1.180213e-31 1758.359
## 48 HIVw+G(4)+I 53 -808.8783 1723.757 1.575570e-31 1759.309
## 45 HIVw 51 -818.7671 1739.534 5.907050e-35 1772.074
## AICcw BIC
## 30 4.812417e-01 1758.816
## 31 4.087478e-01 1759.143
## 32 8.156114e-02 1764.209
## 29 7.994499e-03 1765.125
## 22 8.271839e-03 1766.943
## 23 7.287488e-03 1767.197
## 26 1.201227e-03 1770.802
## 27 1.022124e-03 1771.125
## 24 1.397457e-03 1772.342
## 34 4.703401e-04 1772.677
## 21 1.537658e-04 1773.028
## 35 3.520616e-04 1773.257
## 28 2.036905e-04 1776.194
## 25 1.890911e-05 1777.219
## 36 7.183917e-05 1778.278
## 33 4.117093e-06 1780.268
## 18 1.772577e-13 1816.076
## 19 6.658478e-14 1818.034
## 20 3.004860e-14 1821.468
## 38 3.157767e-15 1824.131
## 39 1.909473e-15 1825.137
## 17 2.760869e-16 1827.119
## 40 5.361198e-16 1829.520
## 37 1.598799e-17 1832.817
## 58 3.832204e-17 1832.954
## 10 2.440441e-17 1833.857
## 59 2.006795e-17 1834.248
## 6 1.428751e-17 1834.928
## 11 1.291949e-17 1835.129
## 66 9.109414e-18 1835.828
## 7 5.900105e-18 1836.696
## 67 3.702955e-18 1837.628
## 60 6.241906e-18 1838.426
## 12 4.137318e-18 1839.249
## 2 1.596910e-18 1839.310
## 8 2.255748e-18 1840.462
## 3 6.132657e-19 1841.224
## 42 5.647633e-19 1841.389
## 68 1.410385e-18 1841.401
## 57 1.415284e-19 1842.271
## 43 3.109663e-19 1842.583
## 9 9.037116e-20 1843.168
## 4 2.427036e-19 1844.921
## 5 2.923065e-20 1845.426
## 65 1.787133e-20 1846.410
## 44 9.599864e-20 1846.776
## 1 2.710800e-21 1850.182
## 41 2.186628e-21 1850.611
## 54 6.780967e-22 1854.839
## 55 4.237250e-22 1855.779
## 50 1.985898e-22 1857.295
## 14 1.099490e-22 1858.477
## 62 1.038420e-22 1858.592
## 51 7.503892e-23 1859.241
## 56 1.055034e-22 1860.402
## 15 3.426835e-23 1860.809
## 63 3.240404e-23 1860.921
## 52 2.938000e-23 1862.959
## 53 3.881649e-24 1863.279
## 16 1.609274e-23 1864.163
## 64 1.519645e-23 1864.278
## 49 3.148771e-25 1868.303
## 13 1.105274e-25 1870.397
## 61 1.048543e-25 1870.502
## 46 5.579368e-31 1896.675
## 47 1.287830e-31 1899.608
## 48 8.007783e-32 1902.400
## 45 1.354228e-34 1911.437Meilleur modele : MtZoa+I
env$`MtZoa+I`## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.778425208675385)Construction arbres
# Matrice de ditance
dm_aa_gr_ext_1 <- dist.ml(mySequences_align_aa_gr_ext_1_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_1 <- NJ(dm_aa_gr_ext_1)Integration des parametres
fit_aa_gr_ext_1 = pml(treeNJ_aa_gr_ext_1, data=mySequences_align_aa_gr_ext_1_phangorn)
fitMtZoa_aa_gr_ext_1 <- update(fit_aa_gr_ext_1, model="MtZoa", inv=0.770287356573796)
fitMtZoa_aa_gr_ext_1 <- optim.pml(fitMtZoa_aa_gr_ext_1, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_aa_gr_ext_1 = bootstrap.pml(fitMtZoa_aa_gr_ext_1, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_1$tree), bs_aa_gr_ext_1, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
L’éléphant d’Afrique + d’Asie
Code NCBI: - MN124272.1 Loxodonta africana voucher - KX395909.1 Elephas maximus voucher
Fusionner avec les cetaces
Sequences_groupe_externe_2 <- c(myNewSequences, myExterneSequences[3:4])ADN
Alignement
mySequences_align_gr_ext_2 = AlignSeqs(Sequences_groupe_externe_2, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.12 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.09 secs
##
## Alignment converged - skipping remaining iteration.Recherche du meilleur modele
mySequences_align_gr_ext_2_ape = as.DNAbin(mySequences_align_gr_ext_2)
mySequences_align_gr_ext_2_phangorn = as.phyDat(mySequences_align_gr_ext_2_ape)
mySequences_gr_ext_2_modelTest = phangorn::modelTest(mySequences_align_gr_ext_2_phangorn)## Model df logLik AIC BIC
## JC 51 -4245.675 8593.349 8826.249
## JC+I 52 -4015.497 8134.993 8372.46
## JC+G(4) 52 -4022.889 8149.778 8387.245
## JC+G(4)+I 53 -4013.284 8132.569 8374.602
## F81 54 -4204.149 8516.297 8762.897
## F81+I 55 -3963.175 8036.349 8287.516
## F81+G(4) 55 -3968.892 8047.783 8298.95
## F81+G(4)+I 56 -3959.909 8031.819 8287.553
## K80 52 -3922.849 7949.699 8187.166
## K80+I 53 -3631.248 7368.497 7610.53
## K80+G(4) 53 -3637.966 7381.932 7623.966
## K80+G(4)+I 54 -3626.102 7360.203 7606.804
## HKY 55 -3881.378 7872.756 8123.923
## HKY+I 56 -3566.651 7245.302 7501.036
## HKY+G(4) 56 -3577.181 7266.363 7522.096
## HKY+G(4)+I 57 -3561.811 7237.623 7497.923
## TrNe 53 -3887.414 7880.829 8122.862
## TrNe+I 54 -3604.951 7317.903 7564.503
## TrNe+G(4) 54 -3615.672 7339.345 7585.945
## TrNe+G(4)+I 55 -3599.083 7308.166 7559.333
## TrN 56 -3868.4 7848.8 8104.533
## TrN+I 57 -3563.434 7240.868 7501.168
## TrN+G(4) 57 -3574.396 7262.793 7523.093
## TrN+G(4)+I 58 -3558.06 7232.12 7496.987
## TPM1 53 -3920.389 7946.777 8188.811
## TPM1+I 54 -3630.827 7369.653 7616.254
## TPM1+G(4) 54 -3635.943 7379.886 7626.486
## TPM1+G(4)+I 55 -3625.547 7361.095 7612.262
## K81 53 -3920.389 7946.777 8188.811
## K81+I 54 -3630.827 7369.653 7616.254
## K81+G(4) 54 -3635.943 7379.886 7626.486
## K81+G(4)+I 55 -3625.547 7361.095 7612.262
## TPM1u 56 -3879.249 7870.499 8126.233
## TPM1u+I 57 -3566.145 7246.29 7506.59
## TPM1u+G(4) 57 -3575.483 7264.966 7525.267
## TPM1u+G(4)+I 58 -3561.21 7238.42 7503.287
## TPM2 53 -3892.302 7890.604 8132.637
## TPM2+I 54 -3622.367 7352.733 7599.334
## TPM2+G(4) 54 -3624.945 7357.89 7604.49
## TPM2+G(4)+I 55 -3616.247 7342.494 7593.661
## TPM2u 56 -3860.517 7833.035 8088.768
## TPM2u+I 57 -3563.003 7240.007 7500.307
## TPM2u+G(4) 57 -3573.225 7260.449 7520.749
## TPM2u+G(4)+I 58 -3558.259 7232.518 7497.385
## TPM3 53 -3918.368 7942.737 8184.771
## TPM3+I 54 -3626.116 7360.232 7606.832
## TPM3+G(4) 54 -3630.034 7368.069 7614.669
## TPM3+G(4)+I 55 -3620.013 7350.026 7601.193
## TPM3u 56 -3877.71 7867.42 8123.154
## TPM3u+I 57 -3562.403 7238.806 7499.106
## TPM3u+G(4) 57 -3570.967 7255.933 7516.234
## TPM3u+G(4)+I 58 -3557.044 7230.088 7494.955
## TIM1e 54 -3885.013 7878.027 8124.627
## TIM1e+I 55 -3604.512 7319.024 7570.191
## TIM1e+G(4) 55 -3613.842 7337.684 7588.851
## TIM1e+G(4)+I 56 -3598.323 7308.646 7564.38
## TIM1 57 -3866.314 7846.628 8106.928
## TIM1+I 58 -3562.927 7241.855 7506.722
## TIM1+G(4) 58 -3572.755 7261.509 7526.376
## TIM1+G(4)+I 59 -3557.441 7232.883 7502.316
## TIM2e 54 -3856.504 7821.008 8067.609
## TIM2e+I 55 -3592.35 7294.7 7545.867
## TIM2e+G(4) 55 -3601.766 7313.531 7564.698
## TIM2e+G(4)+I 56 -3585.821 7283.643 7539.376
## TIM2 57 -3847.515 7809.03 8069.331
## TIM2+I 58 -3559.395 7234.79 7499.657
## TIM2+G(4) 58 -3570.089 7256.177 7521.044
## TIM2+G(4)+I 59 -3554.056 7226.113 7495.546
## TIM3e 54 -3882.944 7873.889 8120.489
## TIM3e+I 55 -3599.471 7308.941 7560.108
## TIM3e+G(4) 55 -3607.741 7325.482 7576.649
## TIM3e+G(4)+I 56 -3592.206 7296.413 7552.146
## TIM3 57 -3864.724 7843.448 8103.748
## TIM3+I 58 -3559.121 7234.242 7499.109
## TIM3+G(4) 58 -3568.115 7252.231 7517.098
## TIM3+G(4)+I 59 -3553.109 7224.217 7493.651
## TVMe 55 -3886.239 7882.478 8133.645
## TVMe+I 56 -3616.587 7345.174 7600.908
## TVMe+G(4) 56 -3615.948 7343.896 7599.63
## TVMe+G(4)+I 57 -3609.189 7332.379 7592.679
## TVM 58 -3855.352 7826.704 8091.571
## TVM+I 59 -3557.821 7233.642 7503.076
## TVM+G(4) 59 -3566.119 7250.237 7519.671
## TVM+G(4)+I 60 -3552.739 7225.478 7499.479
## SYM 56 -3850.34 7812.68 8068.414
## SYM+I 57 -3585.309 7284.619 7544.919
## SYM+G(4) 57 -3592.824 7299.648 7559.948
## SYM+G(4)+I 58 -3578.076 7272.153 7537.02
## GTR 59 -3842.291 7802.582 8072.016
## GTR+I 60 -3554.136 7228.271 7502.272
## GTR+G(4) 60 -3562.925 7245.851 7519.851
## GTR+G(4)+I 61 -3548.397 7218.794 7497.361Trouver le meilleur modele
env <- attr(mySequences_gr_ext_2_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"mySequences_gr_ext_2_modelTest[order(mySequences_gr_ext_2_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3548.397 7218.794 8.736519e-01 7230.449 8.303779e-01
## 76 TIM3+G(4)+I 59 -3553.109 7224.217 5.803466e-02 7235.093 8.144093e-02
## 84 TVM+G(4)+I 60 -3552.739 7225.478 3.089003e-02 7236.740 3.574069e-02
## 68 TIM2+G(4)+I 59 -3554.056 7226.113 2.249549e-02 7236.988 3.156827e-02
## 90 GTR+I 60 -3554.136 7228.271 7.644561e-03 7239.533 8.844987e-03
## 52 TPM3u+G(4)+I 58 -3557.044 7230.088 3.082764e-03 7240.585 5.227777e-03
## 24 TrN+G(4)+I 58 -3558.060 7232.120 1.116052e-03 7242.617 1.892610e-03
## 44 TPM2u+G(4)+I 58 -3558.259 7232.518 9.147047e-04 7243.015 1.551164e-03
## 60 TIM1+G(4)+I 59 -3557.441 7232.883 7.621265e-04 7243.758 1.069504e-03
## 82 TVM+I 59 -3557.821 7233.642 5.212099e-04 7244.518 7.314219e-04
## 74 TIM3+I 58 -3559.121 7234.242 3.862211e-04 7244.739 6.549569e-04
## 66 TIM2+I 58 -3559.395 7234.790 2.936662e-04 7245.287 4.980015e-04
## 16 HKY+G(4)+I 57 -3561.811 7237.623 7.123703e-05 7247.748 1.454527e-04
## 36 TPM1u+G(4)+I 58 -3561.210 7238.420 4.782756e-05 7248.917 8.110636e-05
## 50 TPM3u+I 57 -3562.403 7238.806 3.942134e-05 7248.932 8.049104e-05
## 42 TPM2u+I 57 -3563.003 7240.007 2.162831e-05 7250.132 4.416098e-05
## 22 TrN+I 57 -3563.434 7240.868 1.405997e-05 7250.994 2.870784e-05
## 58 TIM1+I 58 -3562.927 7241.855 8.584212e-06 7252.352 1.455718e-05
## 14 HKY+I 56 -3566.651 7245.302 1.531749e-06 7255.063 3.752049e-06
## 91 GTR+G(4) 60 -3562.925 7245.851 1.164257e-06 7257.112 1.347080e-06
## 34 TPM1u+I 57 -3566.145 7246.290 9.347707e-07 7256.415 1.908628e-06
## 83 TVM+G(4) 59 -3566.119 7250.237 1.298545e-07 7261.113 1.822268e-07
## 75 TIM3+G(4) 58 -3568.115 7252.231 4.793691e-08 7262.727 8.129180e-08
## 51 TPM3u+G(4) 57 -3570.967 7255.933 7.527420e-09 7266.059 1.536959e-08
## 67 TIM2+G(4) 58 -3570.089 7256.177 6.663263e-09 7266.674 1.129962e-08
## 43 TPM2u+G(4) 57 -3573.225 7260.449 7.871177e-10 7270.575 1.607148e-09
## 59 TIM1+G(4) 58 -3572.755 7261.509 4.632645e-10 7272.006 7.856078e-10
## 23 TrN+G(4) 57 -3574.396 7262.793 2.438613e-10 7272.918 4.979194e-10
## 35 TPM1u+G(4) 57 -3575.483 7264.966 8.225174e-11 7275.092 1.679427e-10
## 15 HKY+G(4) 56 -3577.181 7266.363 4.091893e-11 7276.124 1.002317e-10
## 88 SYM+G(4)+I 58 -3578.076 7272.153 2.262426e-12 7282.650 3.836640e-12
## 64 TIM2e+G(4)+I 56 -3585.821 7283.643 7.238146e-15 7293.404 1.772998e-14
## 86 SYM+I 57 -3585.309 7284.619 4.442437e-15 7294.744 9.070630e-15
## 62 TIM2e+I 55 -3592.350 7294.700 2.873928e-17 7304.105 8.414995e-17
## 72 TIM3e+G(4)+I 56 -3592.206 7296.413 1.220756e-17 7306.174 2.990266e-17
## 87 SYM+G(4) 57 -3592.824 7299.648 2.421661e-18 7309.773 4.944581e-18
## 20 TrNe+G(4)+I 55 -3599.083 7308.166 3.423187e-20 7317.571 1.002325e-19
## 56 TIM1e+G(4)+I 56 -3598.323 7308.646 2.692820e-20 7318.407 6.596115e-20
## 70 TIM3e+I 55 -3599.471 7308.941 2.323210e-20 7318.346 6.802468e-20
## 63 TIM2e+G(4) 55 -3601.766 7313.531 2.340967e-21 7322.936 6.854460e-21
## 18 TrNe+I 54 -3604.951 7317.903 2.631265e-22 7326.957 9.176550e-22
## 54 TIM1e+I 55 -3604.512 7319.024 1.501575e-22 7328.429 4.396683e-22
## 71 TIM3e+G(4) 55 -3607.741 7325.482 5.946378e-24 7334.887 1.741127e-23
## 80 TVMe+G(4)+I 57 -3609.189 7332.379 1.890870e-25 7342.505 3.860805e-25
## 55 TIM1e+G(4) 55 -3613.842 7337.684 1.332461e-26 7347.089 3.901509e-26
## 19 TrNe+G(4) 54 -3615.672 7339.345 5.808574e-27 7348.400 2.025743e-26
## 40 TPM2+G(4)+I 55 -3616.247 7342.494 1.202558e-27 7351.899 3.521147e-27
## 79 TVMe+G(4) 56 -3615.948 7343.896 5.966799e-28 7353.658 1.461579e-27
## 78 TVMe+I 56 -3616.587 7345.174 3.149581e-28 7354.935 7.714960e-28
## 48 TPM3+G(4)+I 55 -3620.013 7350.026 2.784179e-29 7359.430 8.152207e-29
## 38 TPM2+I 54 -3622.367 7352.733 7.190944e-30 7361.788 2.507846e-29
## 39 TPM2+G(4) 54 -3624.945 7357.890 5.457204e-31 7366.945 1.903203e-30
## 12 K80+G(4)+I 54 -3626.102 7360.203 1.716521e-31 7369.258 5.986375e-31
## 46 TPM3+I 54 -3626.116 7360.232 1.692037e-31 7369.287 5.900989e-31
## 28 TPM1+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 32 K81+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 47 TPM3+G(4) 54 -3630.034 7368.069 3.362956e-33 7377.124 1.172833e-32
## 10 K80+I 53 -3631.248 7368.497 2.715083e-33 7377.209 1.123781e-32
## 26 TPM1+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 30 K81+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 27 TPM1+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 31 K81+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 11 K80+G(4) 53 -3637.966 7381.932 3.283595e-36 7390.644 1.359090e-35
## 89 GTR 59 -3842.291 7802.582 1.490650e-127 7813.458 2.091852e-127
## 65 TIM2 57 -3847.515 7809.030 5.931339e-129 7819.156 1.211069e-128
## 85 SYM 56 -3850.340 7812.680 9.561794e-130 7822.442 2.342180e-129
## 61 TIM2e 54 -3856.504 7821.008 1.486457e-131 7830.063 5.184027e-131
## 81 TVM 58 -3855.352 7826.704 8.615674e-133 7837.201 1.461053e-132
## 41 TPM2u 56 -3860.517 7833.035 3.635948e-134 7842.796 8.906324e-134
## 73 TIM3 57 -3864.724 7843.448 1.992692e-136 7853.574 4.068706e-136
## 57 TIM1 57 -3866.314 7846.628 4.064257e-137 7856.753 8.298455e-137
## 21 TrN 56 -3868.400 7848.800 1.371896e-137 7858.561 3.360487e-137
## 49 TPM3u 56 -3877.710 7867.420 1.241634e-141 7877.181 3.041407e-141
## 33 TPM1u 56 -3879.249 7870.499 2.663040e-142 7880.260 6.523168e-142
## 13 HKY 55 -3881.378 7872.756 8.615647e-143 7882.161 2.522702e-142
## 69 TIM3e 54 -3882.944 7873.889 4.889345e-143 7882.944 1.705162e-142
## 53 TIM1e 54 -3885.013 7878.027 6.176051e-144 7887.082 2.153901e-143
## 17 TrNe 53 -3887.414 7880.829 1.521693e-144 7889.541 6.298332e-144
## 77 TVMe 55 -3886.239 7882.478 6.669618e-145 7891.883 1.952895e-144
## 37 TPM2 53 -3892.302 7890.604 1.147295e-146 7899.316 4.748687e-146
## 45 TPM3 53 -3918.368 7942.737 5.484169e-158 7951.449 2.269914e-157
## 25 TPM1 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 29 K81 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 9 K80 52 -3922.849 7949.699 1.687822e-159 7958.076 8.261569e-159
## 8 F81+G(4)+I 56 -3959.909 8031.819 2.484339e-177 8041.580 6.085436e-177
## 6 F81+I 55 -3963.175 8036.349 2.578995e-178 8045.754 7.551418e-178
## 7 F81+G(4) 55 -3968.892 8047.783 8.484333e-181 8057.188 2.484252e-180
## 4 JC+G(4)+I 53 -4013.284 8132.569 3.293723e-199 8141.281 1.363282e-198
## 2 JC+I 52 -4015.497 8134.993 9.799726e-200 8143.370 4.796781e-199
## 3 JC+G(4) 52 -4022.889 8149.778 6.034317e-203 8158.155 2.953685e-202
## 5 F81 54 -4204.149 8516.297 1.556283e-282 8525.352 5.427547e-282
## 1 JC 51 -4245.675 8593.349 2.887012e-299 8601.398 1.665264e-298
## BIC
## 92 7497.361
## 76 7493.651
## 84 7499.479
## 68 7495.546
## 90 7502.272
## 52 7494.955
## 24 7496.987
## 44 7497.385
## 60 7502.316
## 82 7503.076
## 74 7499.109
## 66 7499.657
## 16 7497.923
## 36 7503.287
## 50 7499.106
## 42 7500.307
## 22 7501.168
## 58 7506.722
## 14 7501.036
## 91 7519.851
## 34 7506.590
## 83 7519.671
## 75 7517.098
## 51 7516.234
## 67 7521.044
## 43 7520.749
## 59 7526.376
## 23 7523.093
## 35 7525.267
## 15 7522.096
## 88 7537.020
## 64 7539.376
## 86 7544.919
## 62 7545.867
## 72 7552.146
## 87 7559.948
## 20 7559.333
## 56 7564.380
## 70 7560.108
## 63 7564.698
## 18 7564.503
## 54 7570.191
## 71 7576.649
## 80 7592.679
## 55 7588.851
## 19 7585.945
## 40 7593.661
## 79 7599.630
## 78 7600.908
## 48 7601.193
## 38 7599.334
## 39 7604.490
## 12 7606.804
## 46 7606.832
## 28 7612.262
## 32 7612.262
## 47 7614.669
## 10 7610.530
## 26 7616.254
## 30 7616.254
## 27 7626.486
## 31 7626.486
## 11 7623.966
## 89 8072.016
## 65 8069.331
## 85 8068.414
## 61 8067.609
## 81 8091.571
## 41 8088.768
## 73 8103.748
## 57 8106.928
## 21 8104.533
## 49 8123.154
## 33 8126.233
## 13 8123.923
## 69 8120.489
## 53 8124.627
## 17 8122.862
## 77 8133.645
## 37 8132.637
## 45 8184.771
## 25 8188.811
## 29 8188.811
## 9 8187.166
## 8 8287.553
## 6 8287.516
## 7 8298.950
## 4 8374.602
## 2 8372.460
## 3 8387.245
## 5 8762.897
## 1 8826.249mySequences_gr_ext_2_modelTest[order(mySequences_gr_ext_2_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 76 TIM3+G(4)+I 59 -3553.109 7224.217 5.803466e-02 7235.093 8.144093e-02
## 52 TPM3u+G(4)+I 58 -3557.044 7230.088 3.082764e-03 7240.585 5.227777e-03
## 68 TIM2+G(4)+I 59 -3554.056 7226.113 2.249549e-02 7236.988 3.156827e-02
## 24 TrN+G(4)+I 58 -3558.060 7232.120 1.116052e-03 7242.617 1.892610e-03
## 92 GTR+G(4)+I 61 -3548.397 7218.794 8.736519e-01 7230.449 8.303779e-01
## 44 TPM2u+G(4)+I 58 -3558.259 7232.518 9.147047e-04 7243.015 1.551164e-03
## 16 HKY+G(4)+I 57 -3561.811 7237.623 7.123703e-05 7247.748 1.454527e-04
## 50 TPM3u+I 57 -3562.403 7238.806 3.942134e-05 7248.932 8.049104e-05
## 74 TIM3+I 58 -3559.121 7234.242 3.862211e-04 7244.739 6.549569e-04
## 84 TVM+G(4)+I 60 -3552.739 7225.478 3.089003e-02 7236.740 3.574069e-02
## 66 TIM2+I 58 -3559.395 7234.790 2.936662e-04 7245.287 4.980015e-04
## 42 TPM2u+I 57 -3563.003 7240.007 2.162831e-05 7250.132 4.416098e-05
## 14 HKY+I 56 -3566.651 7245.302 1.531749e-06 7255.063 3.752049e-06
## 22 TrN+I 57 -3563.434 7240.868 1.405997e-05 7250.994 2.870784e-05
## 90 GTR+I 60 -3554.136 7228.271 7.644561e-03 7239.533 8.844987e-03
## 60 TIM1+G(4)+I 59 -3557.441 7232.883 7.621265e-04 7243.758 1.069504e-03
## 82 TVM+I 59 -3557.821 7233.642 5.212099e-04 7244.518 7.314219e-04
## 36 TPM1u+G(4)+I 58 -3561.210 7238.420 4.782756e-05 7248.917 8.110636e-05
## 34 TPM1u+I 57 -3566.145 7246.290 9.347707e-07 7256.415 1.908628e-06
## 58 TIM1+I 58 -3562.927 7241.855 8.584212e-06 7252.352 1.455718e-05
## 51 TPM3u+G(4) 57 -3570.967 7255.933 7.527420e-09 7266.059 1.536959e-08
## 75 TIM3+G(4) 58 -3568.115 7252.231 4.793691e-08 7262.727 8.129180e-08
## 83 TVM+G(4) 59 -3566.119 7250.237 1.298545e-07 7261.113 1.822268e-07
## 91 GTR+G(4) 60 -3562.925 7245.851 1.164257e-06 7257.112 1.347080e-06
## 43 TPM2u+G(4) 57 -3573.225 7260.449 7.871177e-10 7270.575 1.607148e-09
## 67 TIM2+G(4) 58 -3570.089 7256.177 6.663263e-09 7266.674 1.129962e-08
## 15 HKY+G(4) 56 -3577.181 7266.363 4.091893e-11 7276.124 1.002317e-10
## 23 TrN+G(4) 57 -3574.396 7262.793 2.438613e-10 7272.918 4.979194e-10
## 35 TPM1u+G(4) 57 -3575.483 7264.966 8.225174e-11 7275.092 1.679427e-10
## 59 TIM1+G(4) 58 -3572.755 7261.509 4.632645e-10 7272.006 7.856078e-10
## 88 SYM+G(4)+I 58 -3578.076 7272.153 2.262426e-12 7282.650 3.836640e-12
## 64 TIM2e+G(4)+I 56 -3585.821 7283.643 7.238146e-15 7293.404 1.772998e-14
## 86 SYM+I 57 -3585.309 7284.619 4.442437e-15 7294.744 9.070630e-15
## 62 TIM2e+I 55 -3592.350 7294.700 2.873928e-17 7304.105 8.414995e-17
## 72 TIM3e+G(4)+I 56 -3592.206 7296.413 1.220756e-17 7306.174 2.990266e-17
## 20 TrNe+G(4)+I 55 -3599.083 7308.166 3.423187e-20 7317.571 1.002325e-19
## 87 SYM+G(4) 57 -3592.824 7299.648 2.421661e-18 7309.773 4.944581e-18
## 70 TIM3e+I 55 -3599.471 7308.941 2.323210e-20 7318.346 6.802468e-20
## 56 TIM1e+G(4)+I 56 -3598.323 7308.646 2.692820e-20 7318.407 6.596115e-20
## 18 TrNe+I 54 -3604.951 7317.903 2.631265e-22 7326.957 9.176550e-22
## 63 TIM2e+G(4) 55 -3601.766 7313.531 2.340967e-21 7322.936 6.854460e-21
## 54 TIM1e+I 55 -3604.512 7319.024 1.501575e-22 7328.429 4.396683e-22
## 71 TIM3e+G(4) 55 -3607.741 7325.482 5.946378e-24 7334.887 1.741127e-23
## 19 TrNe+G(4) 54 -3615.672 7339.345 5.808574e-27 7348.400 2.025743e-26
## 55 TIM1e+G(4) 55 -3613.842 7337.684 1.332461e-26 7347.089 3.901509e-26
## 80 TVMe+G(4)+I 57 -3609.189 7332.379 1.890870e-25 7342.505 3.860805e-25
## 40 TPM2+G(4)+I 55 -3616.247 7342.494 1.202558e-27 7351.899 3.521147e-27
## 38 TPM2+I 54 -3622.367 7352.733 7.190944e-30 7361.788 2.507846e-29
## 79 TVMe+G(4) 56 -3615.948 7343.896 5.966799e-28 7353.658 1.461579e-27
## 78 TVMe+I 56 -3616.587 7345.174 3.149581e-28 7354.935 7.714960e-28
## 48 TPM3+G(4)+I 55 -3620.013 7350.026 2.784179e-29 7359.430 8.152207e-29
## 39 TPM2+G(4) 54 -3624.945 7357.890 5.457204e-31 7366.945 1.903203e-30
## 12 K80+G(4)+I 54 -3626.102 7360.203 1.716521e-31 7369.258 5.986375e-31
## 46 TPM3+I 54 -3626.116 7360.232 1.692037e-31 7369.287 5.900989e-31
## 10 K80+I 53 -3631.248 7368.497 2.715083e-33 7377.209 1.123781e-32
## 28 TPM1+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 32 K81+G(4)+I 55 -3625.547 7361.095 1.099145e-31 7370.500 3.218348e-31
## 47 TPM3+G(4) 54 -3630.034 7368.069 3.362956e-33 7377.124 1.172833e-32
## 26 TPM1+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 30 K81+I 54 -3630.827 7369.653 1.522815e-33 7378.708 5.310824e-33
## 11 K80+G(4) 53 -3637.966 7381.932 3.283595e-36 7390.644 1.359090e-35
## 27 TPM1+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 31 K81+G(4) 54 -3635.943 7379.886 9.135511e-36 7388.940 3.186014e-35
## 61 TIM2e 54 -3856.504 7821.008 1.486457e-131 7830.063 5.184027e-131
## 85 SYM 56 -3850.340 7812.680 9.561794e-130 7822.442 2.342180e-129
## 65 TIM2 57 -3847.515 7809.030 5.931339e-129 7819.156 1.211069e-128
## 89 GTR 59 -3842.291 7802.582 1.490650e-127 7813.458 2.091852e-127
## 41 TPM2u 56 -3860.517 7833.035 3.635948e-134 7842.796 8.906324e-134
## 81 TVM 58 -3855.352 7826.704 8.615674e-133 7837.201 1.461053e-132
## 73 TIM3 57 -3864.724 7843.448 1.992692e-136 7853.574 4.068706e-136
## 21 TrN 56 -3868.400 7848.800 1.371896e-137 7858.561 3.360487e-137
## 57 TIM1 57 -3866.314 7846.628 4.064257e-137 7856.753 8.298455e-137
## 69 TIM3e 54 -3882.944 7873.889 4.889345e-143 7882.944 1.705162e-142
## 17 TrNe 53 -3887.414 7880.829 1.521693e-144 7889.541 6.298332e-144
## 49 TPM3u 56 -3877.710 7867.420 1.241634e-141 7877.181 3.041407e-141
## 13 HKY 55 -3881.378 7872.756 8.615647e-143 7882.161 2.522702e-142
## 53 TIM1e 54 -3885.013 7878.027 6.176051e-144 7887.082 2.153901e-143
## 33 TPM1u 56 -3879.249 7870.499 2.663040e-142 7880.260 6.523168e-142
## 37 TPM2 53 -3892.302 7890.604 1.147295e-146 7899.316 4.748687e-146
## 77 TVMe 55 -3886.239 7882.478 6.669618e-145 7891.883 1.952895e-144
## 45 TPM3 53 -3918.368 7942.737 5.484169e-158 7951.449 2.269914e-157
## 9 K80 52 -3922.849 7949.699 1.687822e-159 7958.076 8.261569e-159
## 25 TPM1 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 29 K81 53 -3920.389 7946.777 7.272961e-159 7955.490 3.010300e-158
## 6 F81+I 55 -3963.175 8036.349 2.578995e-178 8045.754 7.551418e-178
## 8 F81+G(4)+I 56 -3959.909 8031.819 2.484339e-177 8041.580 6.085436e-177
## 7 F81+G(4) 55 -3968.892 8047.783 8.484333e-181 8057.188 2.484252e-180
## 2 JC+I 52 -4015.497 8134.993 9.799726e-200 8143.370 4.796781e-199
## 4 JC+G(4)+I 53 -4013.284 8132.569 3.293723e-199 8141.281 1.363282e-198
## 3 JC+G(4) 52 -4022.889 8149.778 6.034317e-203 8158.155 2.953685e-202
## 5 F81 54 -4204.149 8516.297 1.556283e-282 8525.352 5.427547e-282
## 1 JC 51 -4245.675 8593.349 2.887012e-299 8601.398 1.665264e-298
## BIC
## 76 7493.651
## 52 7494.955
## 68 7495.546
## 24 7496.987
## 92 7497.361
## 44 7497.385
## 16 7497.923
## 50 7499.106
## 74 7499.109
## 84 7499.479
## 66 7499.657
## 42 7500.307
## 14 7501.036
## 22 7501.168
## 90 7502.272
## 60 7502.316
## 82 7503.076
## 36 7503.287
## 34 7506.590
## 58 7506.722
## 51 7516.234
## 75 7517.098
## 83 7519.671
## 91 7519.851
## 43 7520.749
## 67 7521.044
## 15 7522.096
## 23 7523.093
## 35 7525.267
## 59 7526.376
## 88 7537.020
## 64 7539.376
## 86 7544.919
## 62 7545.867
## 72 7552.146
## 20 7559.333
## 87 7559.948
## 70 7560.108
## 56 7564.380
## 18 7564.503
## 63 7564.698
## 54 7570.191
## 71 7576.649
## 19 7585.945
## 55 7588.851
## 80 7592.679
## 40 7593.661
## 38 7599.334
## 79 7599.630
## 78 7600.908
## 48 7601.193
## 39 7604.490
## 12 7606.804
## 46 7606.832
## 10 7610.530
## 28 7612.262
## 32 7612.262
## 47 7614.669
## 26 7616.254
## 30 7616.254
## 11 7623.966
## 27 7626.486
## 31 7626.486
## 61 8067.609
## 85 8068.414
## 65 8069.331
## 89 8072.016
## 41 8088.768
## 81 8091.571
## 73 8103.748
## 21 8104.533
## 57 8106.928
## 69 8120.489
## 17 8122.862
## 49 8123.154
## 13 8123.923
## 53 8124.627
## 33 8126.233
## 37 8132.637
## 77 8133.645
## 45 8184.771
## 9 8187.166
## 25 8188.811
## 29 8188.811
## 6 8287.516
## 8 8287.553
## 7 8298.950
## 2 8372.460
## 4 8374.602
## 3 8387.245
## 5 8762.897
## 1 8826.249Meilleur modele: TIM3+G(4)+I
env$`TIM3+G(4)+I`## pml(tree = `tree_TIM3+G(4)+I`, data = data, bf = c(0.269455971803763,
## 0.265704053209027, 0.168154169745893, 0.296685805241317), Q = c(0.217532543290871,
## 10.3742034797635, 1, 0.217532543290871, 15.4906238569354, 1),
## model = "TIM3", inv = 0.578802070346248, k = 4, shape = 3.51925700550295)Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_2 = dist.logDet(mySequences_align_gr_ext_2_phangorn) # TIM3 existe pas donc utilise dist.logDet
# Construction arbre NJ
treeNJ_gr_ext_2 <- NJ(mySequences_align_gr_ext_2)
# Visualisation
plot(treeNJ_gr_ext_2, main="Arbre NJ Groupe externe 2")
Integration des parametres
fit_gr_ext_2 = pml(treeNJ_gr_ext_2, data=mySequences_align_gr_ext_2_phangorn)
fitTIM3_gr_ext_2 <- update(fit_gr_ext_2, model="TIM3", k=4, inv=0.57880211554897, shape=3.51926023272271)
fitTIM3_gr_ext_2 <- optim.pml(fitTIM3_gr_ext_2, model="TIM3", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_gr_ext_2 = bootstrap.pml(fitTIM3_gr_ext_2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM3_gr_ext_2$tree), bs_gr_ext_2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
AA
Alignement
mySequences_align_aa_gr_ext_2 = AlignTranslation(Sequences_groupe_externe_2,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Alignment converged - skipping remaining iteration.Conversion
mySequences_align_aa_gr_ext_2_ape = as.AAbin(mySequences_align_aa_gr_ext_2)
mySequences_align_aa_gr_ext_2_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_2_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Recherche du meilleur modele
mySequences_align_aa_gr_ext_2_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_2_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 51 -882.803 1867.606 2043.39
## WAG+I 52 -873.045 1850.09 2029.32
## WAG+G(4) 52 -873.4912 1850.982 2030.213
## WAG+G(4)+I 53 -873.0976 1852.195 2034.872
## JTT 51 -878.4193 1858.839 2034.622
## JTT+I 52 -868.8141 1841.628 2020.859
## JTT+G(4) 52 -869.2302 1842.46 2021.691
## JTT+G(4)+I 53 -868.842 1843.684 2026.361
## LG 51 -878.6655 1859.331 2035.115
## LG+I 52 -869.9485 1843.897 2023.127
## LG+G(4) 52 -870.1609 1844.322 2023.552
## LG+G(4)+I 53 -870.0532 1846.106 2028.783
## Dayhoff 51 -893.5243 1889.049 2064.832
## Dayhoff+I 52 -882.9789 1869.958 2049.188
## Dayhoff+G(4) 52 -883.5904 1871.181 2050.411
## Dayhoff+G(4)+I 53 -883.0527 1872.105 2054.782
## cpREV 51 -870.6275 1843.255 2019.039
## cpREV+I 52 -860.9882 1825.976 2005.207
## cpREV+G(4) 52 -861.3964 1826.793 2006.023
## cpREV+G(4)+I 53 -861.1584 1828.317 2010.994
## mtmam 51 -838.8119 1779.624 1955.407
## mtmam+I 52 -832.0069 1768.014 1947.244
## mtmam+G(4) 52 -832.0989 1768.198 1947.428
## mtmam+G(4)+I 53 -832.0177 1770.035 1952.712
## mtArt 51 -843.3283 1788.657 1964.44
## mtArt+I 52 -835.9722 1775.944 1955.175
## mtArt+G(4) 52 -836.0526 1776.105 1955.336
## mtArt+G(4)+I 53 -835.9819 1777.964 1960.641
## MtZoa 51 -836.5178 1775.036 1950.819
## MtZoa+I 52 -829.337 1762.674 1941.904
## MtZoa+G(4) 52 -829.4184 1762.837 1942.067
## MtZoa+G(4)+I 53 -829.3528 1764.706 1947.383
## mtREV24 51 -846.478 1794.956 1970.74
## mtREV24+I 52 -838.5859 1781.172 1960.402
## mtREV24+G(4) 52 -838.6387 1781.277 1960.508
## mtREV24+G(4)+I 53 -838.755 1783.51 1966.187
## VT 51 -875.5437 1853.087 2028.871
## VT+I 52 -866.9042 1837.808 2017.039
## VT+G(4) 52 -867.1174 1838.235 2017.465
## VT+G(4)+I 53 -867.0605 1840.121 2022.798
## RtREV 51 -883.3528 1868.706 2044.489
## RtREV+I 52 -874.7996 1853.599 2032.83
## RtREV+G(4) 52 -874.9566 1853.913 2033.144
## RtREV+G(4)+I 53 -874.9087 1855.817 2038.494
## HIVw 51 -912.015 1926.03 2101.814
## HIVw+I 52 -900.3747 1904.749 2083.98
## HIVw+G(4) 52 -901.1 1906.2 2085.43
## HIVw+G(4)+I 53 -900.216 1906.432 2089.109
## HIVb 51 -890.6387 1883.277 2059.061
## HIVb+I 52 -880.5819 1865.164 2044.394
## HIVb+G(4) 52 -881.0801 1866.16 2045.39
## HIVb+G(4)+I 53 -880.6306 1867.261 2049.938
## FLU 51 -884.9149 1871.83 2047.613
## FLU+I 52 -876.2556 1856.511 2035.742
## FLU+G(4) 52 -876.4943 1856.989 2036.219
## FLU+G(4)+I 53 -876.3837 1858.767 2041.444
## Blosum62 51 -880.9273 1863.855 2039.638
## Blosum62+I 52 -872.0477 1848.095 2027.326
## Blosum62+G(4) 52 -872.2876 1848.575 2027.806
## Blosum62+G(4)+I 53 -872.1772 1850.354 2033.031
## Dayhoff_DCMut 51 -893.5996 1889.199 2064.983
## Dayhoff_DCMut+I 52 -883.0602 1870.12 2049.351
## Dayhoff_DCMut+G(4) 52 -883.671 1871.342 2050.572
## Dayhoff_DCMut+G(4)+I 53 -883.135 1872.27 2054.947
## JTT_DCMut 51 -879.0681 1860.136 2035.92
## JTT_DCMut+I 52 -869.4004 1842.801 2022.031
## JTT_DCMut+G(4) 52 -869.8305 1843.661 2022.891
## JTT_DCMut+G(4)+I 53 -869.4308 1844.862 2027.539Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_2_modeltest, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"mySequences_align_aa_gr_ext_2_modeltest[order(mySequences_align_aa_gr_ext_2_modeltest$AIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -829.3370 1762.674 4.086509e-01 1793.467
## 31 MtZoa+G(4) 52 -829.4184 1762.837 3.767111e-01 1793.630
## 32 MtZoa+G(4)+I 53 -829.3528 1764.706 1.479743e-01 1796.863
## 22 mtmam+I 52 -832.0069 1768.014 2.830140e-02 1798.807
## 23 mtmam+G(4) 52 -832.0989 1768.198 2.581390e-02 1798.991
## 24 mtmam+G(4)+I 53 -832.0177 1770.035 1.030049e-02 1802.193
## 29 MtZoa 51 -836.5178 1775.036 8.454015e-04 1804.502
## 26 mtArt+I 52 -835.9722 1775.944 5.366910e-04 1806.738
## 27 mtArt+G(4) 52 -836.0526 1776.105 4.952221e-04 1806.898
## 28 mtArt+G(4)+I 53 -835.9819 1777.964 1.955327e-04 1810.121
## 21 mtmam 51 -838.8119 1779.624 8.525823e-05 1809.091
## 34 mtREV24+I 52 -838.5859 1781.172 3.931862e-05 1811.965
## 35 mtREV24+G(4) 52 -838.6387 1781.277 3.729804e-05 1812.071
## 36 mtREV24+G(4)+I 53 -838.7550 1783.510 1.221371e-05 1815.667
## 25 mtArt 51 -843.3283 1788.657 9.317811e-07 1818.123
## 33 mtREV24 51 -846.4780 1794.956 3.993832e-08 1824.423
## 18 cpREV+I 52 -860.9882 1825.976 7.335240e-15 1856.770
## 19 cpREV+G(4) 52 -861.3964 1826.793 4.876822e-15 1857.586
## 20 cpREV+G(4)+I 53 -861.1584 1828.317 2.276193e-15 1860.474
## 38 VT+I 52 -866.9042 1837.808 1.977559e-17 1868.602
## 39 VT+G(4) 52 -867.1174 1838.235 1.597761e-17 1869.028
## 40 VT+G(4)+I 53 -867.0605 1840.121 6.221998e-18 1872.278
## 6 JTT+I 52 -868.8141 1841.628 2.928622e-18 1872.421
## 7 JTT+G(4) 52 -869.2302 1842.460 1.931736e-18 1873.254
## 66 JTT_DCMut+I 52 -869.4004 1842.801 1.629502e-18 1873.594
## 17 cpREV 51 -870.6275 1843.255 1.298399e-18 1872.722
## 67 JTT_DCMut+G(4) 52 -869.8305 1843.661 1.059877e-18 1874.454
## 8 JTT+G(4)+I 53 -868.8420 1843.684 1.047731e-18 1875.841
## 10 LG+I 52 -869.9485 1843.897 9.419195e-19 1874.690
## 11 LG+G(4) 52 -870.1609 1844.322 7.616255e-19 1875.115
## 68 JTT_DCMut+G(4)+I 53 -869.4308 1844.862 5.814963e-19 1877.019
## 12 LG+G(4)+I 53 -870.0532 1846.106 3.120693e-19 1878.264
## 58 Blosum62+I 52 -872.0477 1848.095 1.154323e-19 1878.889
## 59 Blosum62+G(4) 52 -872.2876 1848.575 9.080846e-20 1879.369
## 2 WAG+I 52 -873.0450 1850.090 4.257993e-20 1880.883
## 60 Blosum62+G(4)+I 53 -872.1772 1850.354 3.730746e-20 1882.512
## 3 WAG+G(4) 52 -873.4912 1850.982 2.725396e-20 1881.776
## 4 WAG+G(4)+I 53 -873.0976 1852.195 1.486175e-20 1884.352
## 37 VT 51 -875.5437 1853.087 9.513497e-21 1882.554
## 42 RtREV+I 52 -874.7996 1853.599 7.365235e-21 1884.393
## 43 RtREV+G(4) 52 -874.9566 1853.913 6.295037e-21 1884.707
## 44 RtREV+G(4)+I 53 -874.9087 1855.817 2.429545e-21 1887.975
## 54 FLU+I 52 -876.2556 1856.511 1.717291e-21 1887.305
## 55 FLU+G(4) 52 -876.4943 1856.989 1.352725e-21 1887.782
## 56 FLU+G(4)+I 53 -876.3837 1858.767 5.558368e-22 1890.925
## 5 JTT 51 -878.4193 1858.839 5.363792e-22 1888.305
## 9 LG 51 -878.6655 1859.331 4.193163e-22 1888.798
## 65 JTT_DCMut 51 -879.0681 1860.136 2.803550e-22 1889.603
## 57 Blosum62 51 -880.9273 1863.855 4.367880e-23 1893.321
## 50 HIVb+I 52 -880.5819 1865.164 2.269622e-23 1895.957
## 51 HIVb+G(4) 52 -881.0801 1866.160 1.379187e-23 1896.953
## 52 HIVb+G(4)+I 53 -880.6306 1867.261 7.953253e-24 1899.418
## 1 WAG 51 -882.8030 1867.606 6.693393e-24 1897.073
## 41 RtREV 51 -883.3528 1868.706 3.862618e-24 1898.172
## 14 Dayhoff+I 52 -882.9789 1869.958 2.065250e-24 1900.751
## 62 Dayhoff_DCMut+I 52 -883.0602 1870.120 1.903931e-24 1900.914
## 15 Dayhoff+G(4) 52 -883.5904 1871.181 1.120450e-24 1901.974
## 63 Dayhoff_DCMut+G(4) 52 -883.6710 1871.342 1.033650e-24 1902.135
## 53 FLU 51 -884.9149 1871.830 8.099834e-25 1901.296
## 16 Dayhoff+G(4)+I 53 -883.0527 1872.105 7.057312e-25 1904.263
## 64 Dayhoff_DCMut+G(4)+I 53 -883.1350 1872.270 6.499520e-25 1904.427
## 49 HIVb 51 -890.6387 1883.277 2.646449e-27 1912.744
## 13 Dayhoff 51 -893.5243 1889.049 1.477272e-28 1918.515
## 61 Dayhoff_DCMut 51 -893.5996 1889.199 1.370038e-28 1918.666
## 46 HIVw+I 52 -900.3747 1904.749 5.755323e-32 1935.543
## 47 HIVw+G(4) 52 -901.1000 1906.200 2.786460e-32 1936.993
## 48 HIVw+G(4)+I 53 -900.2160 1906.432 2.481503e-32 1938.589
## 45 HIVw 51 -912.0150 1926.030 1.377353e-36 1955.497
## AICcw BIC
## 30 4.429707e-01 1941.904
## 31 4.083485e-01 1942.067
## 32 8.109954e-02 1947.383
## 22 3.067824e-02 1947.244
## 23 2.798184e-02 1947.428
## 24 5.645340e-03 1952.712
## 29 1.778932e-03 1950.819
## 26 5.817640e-04 1955.175
## 27 5.368125e-04 1955.336
## 28 1.071646e-04 1960.641
## 21 1.794043e-04 1955.407
## 34 4.262072e-05 1960.402
## 35 4.043044e-05 1960.508
## 36 6.693906e-06 1966.187
## 25 1.960696e-06 1964.440
## 33 8.404004e-08 1970.740
## 18 7.951277e-15 2005.207
## 19 5.286393e-15 2006.023
## 20 1.247502e-15 2010.994
## 38 2.143641e-17 2017.039
## 39 1.731946e-17 2017.465
## 40 3.410059e-18 2022.798
## 6 3.174577e-18 2020.859
## 7 2.093969e-18 2021.691
## 66 1.766353e-18 2022.031
## 17 2.732151e-18 2019.039
## 67 1.148889e-18 2022.891
## 8 5.742248e-19 2026.361
## 10 1.021025e-18 2023.127
## 11 8.255892e-19 2023.552
## 68 3.186978e-19 2027.539
## 12 1.710343e-19 2028.783
## 58 1.251266e-19 2027.326
## 59 9.843484e-20 2027.806
## 2 4.615592e-20 2029.320
## 60 2.044691e-20 2033.031
## 3 2.954284e-20 2030.213
## 4 8.145204e-21 2034.872
## 37 2.001874e-20 2028.871
## 42 7.983791e-21 2032.830
## 43 6.823714e-21 2033.144
## 44 1.331549e-21 2038.494
## 54 1.861515e-21 2035.742
## 55 1.466331e-21 2036.219
## 56 3.046347e-22 2041.444
## 5 1.128674e-21 2034.622
## 9 8.823446e-22 2035.115
## 65 5.899357e-22 2035.920
## 57 9.191094e-23 2039.638
## 50 2.460232e-23 2044.394
## 51 1.495015e-23 2045.390
## 52 4.358900e-24 2049.938
## 1 1.408454e-23 2043.390
## 41 8.127898e-24 2044.489
## 14 2.238696e-24 2049.188
## 62 2.063829e-24 2049.351
## 15 1.214549e-24 2050.411
## 63 1.120460e-24 2050.572
## 53 1.704404e-24 2047.613
## 16 3.867866e-25 2054.782
## 64 3.562160e-25 2054.947
## 49 5.568779e-27 2059.061
## 13 3.108543e-28 2064.832
## 61 2.882897e-28 2064.983
## 46 6.238673e-32 2083.980
## 47 3.020476e-32 2085.430
## 48 1.360025e-32 2089.109
## 45 2.898289e-36 2101.814mySequences_align_aa_gr_ext_2_modeltest[order(mySequences_align_aa_gr_ext_2_modeltest$BIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -829.3370 1762.674 4.086509e-01 1793.467
## 31 MtZoa+G(4) 52 -829.4184 1762.837 3.767111e-01 1793.630
## 22 mtmam+I 52 -832.0069 1768.014 2.830140e-02 1798.807
## 32 MtZoa+G(4)+I 53 -829.3528 1764.706 1.479743e-01 1796.863
## 23 mtmam+G(4) 52 -832.0989 1768.198 2.581390e-02 1798.991
## 29 MtZoa 51 -836.5178 1775.036 8.454015e-04 1804.502
## 24 mtmam+G(4)+I 53 -832.0177 1770.035 1.030049e-02 1802.193
## 26 mtArt+I 52 -835.9722 1775.944 5.366910e-04 1806.738
## 27 mtArt+G(4) 52 -836.0526 1776.105 4.952221e-04 1806.898
## 21 mtmam 51 -838.8119 1779.624 8.525823e-05 1809.091
## 34 mtREV24+I 52 -838.5859 1781.172 3.931862e-05 1811.965
## 35 mtREV24+G(4) 52 -838.6387 1781.277 3.729804e-05 1812.071
## 28 mtArt+G(4)+I 53 -835.9819 1777.964 1.955327e-04 1810.121
## 25 mtArt 51 -843.3283 1788.657 9.317811e-07 1818.123
## 36 mtREV24+G(4)+I 53 -838.7550 1783.510 1.221371e-05 1815.667
## 33 mtREV24 51 -846.4780 1794.956 3.993832e-08 1824.423
## 18 cpREV+I 52 -860.9882 1825.976 7.335240e-15 1856.770
## 19 cpREV+G(4) 52 -861.3964 1826.793 4.876822e-15 1857.586
## 20 cpREV+G(4)+I 53 -861.1584 1828.317 2.276193e-15 1860.474
## 38 VT+I 52 -866.9042 1837.808 1.977559e-17 1868.602
## 39 VT+G(4) 52 -867.1174 1838.235 1.597761e-17 1869.028
## 17 cpREV 51 -870.6275 1843.255 1.298399e-18 1872.722
## 6 JTT+I 52 -868.8141 1841.628 2.928622e-18 1872.421
## 7 JTT+G(4) 52 -869.2302 1842.460 1.931736e-18 1873.254
## 66 JTT_DCMut+I 52 -869.4004 1842.801 1.629502e-18 1873.594
## 40 VT+G(4)+I 53 -867.0605 1840.121 6.221998e-18 1872.278
## 67 JTT_DCMut+G(4) 52 -869.8305 1843.661 1.059877e-18 1874.454
## 10 LG+I 52 -869.9485 1843.897 9.419195e-19 1874.690
## 11 LG+G(4) 52 -870.1609 1844.322 7.616255e-19 1875.115
## 8 JTT+G(4)+I 53 -868.8420 1843.684 1.047731e-18 1875.841
## 58 Blosum62+I 52 -872.0477 1848.095 1.154323e-19 1878.889
## 68 JTT_DCMut+G(4)+I 53 -869.4308 1844.862 5.814963e-19 1877.019
## 59 Blosum62+G(4) 52 -872.2876 1848.575 9.080846e-20 1879.369
## 12 LG+G(4)+I 53 -870.0532 1846.106 3.120693e-19 1878.264
## 37 VT 51 -875.5437 1853.087 9.513497e-21 1882.554
## 2 WAG+I 52 -873.0450 1850.090 4.257993e-20 1880.883
## 3 WAG+G(4) 52 -873.4912 1850.982 2.725396e-20 1881.776
## 42 RtREV+I 52 -874.7996 1853.599 7.365235e-21 1884.393
## 60 Blosum62+G(4)+I 53 -872.1772 1850.354 3.730746e-20 1882.512
## 43 RtREV+G(4) 52 -874.9566 1853.913 6.295037e-21 1884.707
## 5 JTT 51 -878.4193 1858.839 5.363792e-22 1888.305
## 4 WAG+G(4)+I 53 -873.0976 1852.195 1.486175e-20 1884.352
## 9 LG 51 -878.6655 1859.331 4.193163e-22 1888.798
## 54 FLU+I 52 -876.2556 1856.511 1.717291e-21 1887.305
## 65 JTT_DCMut 51 -879.0681 1860.136 2.803550e-22 1889.603
## 55 FLU+G(4) 52 -876.4943 1856.989 1.352725e-21 1887.782
## 44 RtREV+G(4)+I 53 -874.9087 1855.817 2.429545e-21 1887.975
## 57 Blosum62 51 -880.9273 1863.855 4.367880e-23 1893.321
## 56 FLU+G(4)+I 53 -876.3837 1858.767 5.558368e-22 1890.925
## 1 WAG 51 -882.8030 1867.606 6.693393e-24 1897.073
## 50 HIVb+I 52 -880.5819 1865.164 2.269622e-23 1895.957
## 41 RtREV 51 -883.3528 1868.706 3.862618e-24 1898.172
## 51 HIVb+G(4) 52 -881.0801 1866.160 1.379187e-23 1896.953
## 53 FLU 51 -884.9149 1871.830 8.099834e-25 1901.296
## 14 Dayhoff+I 52 -882.9789 1869.958 2.065250e-24 1900.751
## 62 Dayhoff_DCMut+I 52 -883.0602 1870.120 1.903931e-24 1900.914
## 52 HIVb+G(4)+I 53 -880.6306 1867.261 7.953253e-24 1899.418
## 15 Dayhoff+G(4) 52 -883.5904 1871.181 1.120450e-24 1901.974
## 63 Dayhoff_DCMut+G(4) 52 -883.6710 1871.342 1.033650e-24 1902.135
## 16 Dayhoff+G(4)+I 53 -883.0527 1872.105 7.057312e-25 1904.263
## 64 Dayhoff_DCMut+G(4)+I 53 -883.1350 1872.270 6.499520e-25 1904.427
## 49 HIVb 51 -890.6387 1883.277 2.646449e-27 1912.744
## 13 Dayhoff 51 -893.5243 1889.049 1.477272e-28 1918.515
## 61 Dayhoff_DCMut 51 -893.5996 1889.199 1.370038e-28 1918.666
## 46 HIVw+I 52 -900.3747 1904.749 5.755323e-32 1935.543
## 47 HIVw+G(4) 52 -901.1000 1906.200 2.786460e-32 1936.993
## 48 HIVw+G(4)+I 53 -900.2160 1906.432 2.481503e-32 1938.589
## 45 HIVw 51 -912.0150 1926.030 1.377353e-36 1955.497
## AICcw BIC
## 30 4.429707e-01 1941.904
## 31 4.083485e-01 1942.067
## 22 3.067824e-02 1947.244
## 32 8.109954e-02 1947.383
## 23 2.798184e-02 1947.428
## 29 1.778932e-03 1950.819
## 24 5.645340e-03 1952.712
## 26 5.817640e-04 1955.175
## 27 5.368125e-04 1955.336
## 21 1.794043e-04 1955.407
## 34 4.262072e-05 1960.402
## 35 4.043044e-05 1960.508
## 28 1.071646e-04 1960.641
## 25 1.960696e-06 1964.440
## 36 6.693906e-06 1966.187
## 33 8.404004e-08 1970.740
## 18 7.951277e-15 2005.207
## 19 5.286393e-15 2006.023
## 20 1.247502e-15 2010.994
## 38 2.143641e-17 2017.039
## 39 1.731946e-17 2017.465
## 17 2.732151e-18 2019.039
## 6 3.174577e-18 2020.859
## 7 2.093969e-18 2021.691
## 66 1.766353e-18 2022.031
## 40 3.410059e-18 2022.798
## 67 1.148889e-18 2022.891
## 10 1.021025e-18 2023.127
## 11 8.255892e-19 2023.552
## 8 5.742248e-19 2026.361
## 58 1.251266e-19 2027.326
## 68 3.186978e-19 2027.539
## 59 9.843484e-20 2027.806
## 12 1.710343e-19 2028.783
## 37 2.001874e-20 2028.871
## 2 4.615592e-20 2029.320
## 3 2.954284e-20 2030.213
## 42 7.983791e-21 2032.830
## 60 2.044691e-20 2033.031
## 43 6.823714e-21 2033.144
## 5 1.128674e-21 2034.622
## 4 8.145204e-21 2034.872
## 9 8.823446e-22 2035.115
## 54 1.861515e-21 2035.742
## 65 5.899357e-22 2035.920
## 55 1.466331e-21 2036.219
## 44 1.331549e-21 2038.494
## 57 9.191094e-23 2039.638
## 56 3.046347e-22 2041.444
## 1 1.408454e-23 2043.390
## 50 2.460232e-23 2044.394
## 41 8.127898e-24 2044.489
## 51 1.495015e-23 2045.390
## 53 1.704404e-24 2047.613
## 14 2.238696e-24 2049.188
## 62 2.063829e-24 2049.351
## 52 4.358900e-24 2049.938
## 15 1.214549e-24 2050.411
## 63 1.120460e-24 2050.572
## 16 3.867866e-25 2054.782
## 64 3.562160e-25 2054.947
## 49 5.568779e-27 2059.061
## 13 3.108543e-28 2064.832
## 61 2.882897e-28 2064.983
## 46 6.238673e-32 2083.980
## 47 3.020476e-32 2085.430
## 48 1.360025e-32 2089.109
## 45 2.898289e-36 2101.814Meilleur modele : MtZoa+I
env$`MtZoa+I`## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.733691146551266)Construction arbres
# Matrice de ditance
dm_aa_gr_ext_2 <- dist.ml(mySequences_align_aa_gr_ext_2_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_2 <- NJ(dm_aa_gr_ext_2)Integration des parametres
fit_aa_gr_ext_2 = pml(treeNJ_aa_gr_ext_2, data=mySequences_align_aa_gr_ext_2_phangorn)
fitMtZoa_aa_gr_ext_2 <- update(fit_aa_gr_ext_2, model="MtZoa", inv=0.737372323527904)
fitMtZoa_aa_gr_ext_2 <- optim.pml(fitMtZoa_aa_gr_ext_2, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_aa_gr_ext_2 = bootstrap.pml(fitMtZoa_aa_gr_ext_2, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_2$tree), bs_aa_gr_ext_2, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
hippopotame + hippopotame nain
Code NCBI: - NC_000889.1 Hippopotamus amphibius mitochondrion - NC_020697.1 Hexaprotodon liberiensis isolate
Fusionner avec les cetaces
Sequences_groupe_externe_3 <- c(myNewSequences, myExterneSequences[5:6])ADN
Alignement
mySequences_align_gr_ext_3 = AlignSeqs(Sequences_groupe_externe_3, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 11-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.54 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.3 secs
##
## Alignment converged - skipping remaining iteration.Recherche du meilleur modele
mySequences_align_gr_ext_3_ape = as.DNAbin(mySequences_align_gr_ext_3)
mySequences_align_gr_ext_3_phangorn = as.phyDat(mySequences_align_gr_ext_3_ape)
mySequences_gr_ext_3_modelTest = phangorn::modelTest(mySequences_align_gr_ext_3_phangorn)## Model df logLik AIC BIC
## JC 51 -30545.14 61192.28 61585.27
## JC+I 52 -30308.99 60721.98 61122.67
## JC+G(4) 52 -30321.38 60746.77 61147.46
## JC+G(4)+I 53 -30308.43 60722.85 61131.25
## F81 54 -29849.89 59807.78 60223.89
## F81+I 55 -29596.55 59303.09 59726.9
## F81+G(4) 55 -29609.53 59329.06 59752.87
## F81+G(4)+I 56 -29596.04 59304.08 59735.6
## K80 52 -29553.92 59211.84 59612.54
## K80+I 53 -29273.48 58652.97 59061.37
## K80+G(4) 53 -29278.31 58662.63 59071.03
## K80+G(4)+I 54 -29268.61 58645.21 59061.32
## HKY 55 -28822.41 57754.82 58178.63
## HKY+I 56 -28488.1 57088.2 57519.72
## HKY+G(4) 56 -28499.12 57110.24 57541.76
## HKY+G(4)+I 57 -28485.21 57084.42 57523.64
## TrNe 53 -29525.37 59156.74 59565.14
## TrNe+I 54 -29251.79 58611.58 59027.68
## TrNe+G(4) 54 -29259.18 58626.36 59042.47
## TrNe+G(4)+I 55 -29247.28 58604.55 59028.36
## TrN 56 -28820.25 57752.49 58184.01
## TrN+I 57 -28488.03 57090.06 57529.28
## TrN+G(4) 57 -28499.11 57112.22 57551.44
## TrN+G(4)+I 58 -28485.19 57086.38 57533.3
## TPM1 53 -29553.92 59213.84 59622.24
## TPM1+I 54 -29273.46 58654.92 59071.03
## TPM1+G(4) 54 -29278.31 58664.62 59080.72
## TPM1+G(4)+I 55 -29268.6 58647.21 59071.02
## K81 53 -29553.92 59213.84 59622.24
## K81+I 54 -29273.46 58654.92 59071.03
## K81+G(4) 54 -29278.31 58664.62 59080.72
## K81+G(4)+I 55 -29268.6 58647.21 59071.02
## TPM1u 56 -28822.4 57756.8 58188.31
## TPM1u+I 57 -28488.08 57090.17 57529.39
## TPM1u+G(4) 57 -28499.07 57112.14 57551.36
## TPM1u+G(4)+I 58 -28485.18 57086.36 57533.29
## TPM2 53 -29530.37 59166.73 59575.13
## TPM2+I 54 -29263.02 58634.04 59050.14
## TPM2+G(4) 54 -29265.82 58639.65 59055.75
## TPM2+G(4)+I 55 -29256.56 58623.13 59046.94
## TPM2u 56 -28813.36 57738.72 58170.23
## TPM2u+I 57 -28486.89 57087.79 57527.01
## TPM2u+G(4) 57 -28497.79 57109.58 57548.8
## TPM2u+G(4)+I 58 -28484.1 57084.21 57531.14
## TPM3 53 -29553.39 59212.79 59621.19
## TPM3+I 54 -29272.2 58652.39 59068.5
## TPM3+G(4) 54 -29276.93 58661.87 59077.97
## TPM3+G(4)+I 55 -29267.19 58644.37 59068.18
## TPM3u 56 -28821.67 57755.34 58186.86
## TPM3u+I 57 -28486.73 57087.45 57526.67
## TPM3u+G(4) 57 -28497.5 57109 57548.22
## TPM3u+G(4)+I 58 -28483.74 57083.48 57530.41
## TIM1e 54 -29525.37 59158.74 59574.85
## TIM1e+I 55 -29251.77 58613.55 59037.36
## TIM1e+G(4) 55 -29259.18 58628.36 59052.17
## TIM1e+G(4)+I 56 -29247.27 58606.54 59038.06
## TIM1 57 -28820.23 57754.47 58193.69
## TIM1+I 58 -28488.01 57092.03 57538.95
## TIM1+G(4) 58 -28499.06 57114.12 57561.04
## TIM1+G(4)+I 59 -28485.16 57088.32 57542.96
## TIM2e 54 -29501.48 59110.95 59527.06
## TIM2e+I 55 -29238.43 58586.86 59010.67
## TIM2e+G(4) 55 -29245.96 58601.92 59025.73
## TIM2e+G(4)+I 56 -29234.19 58580.37 59011.89
## TIM2 57 -28811.16 57736.33 58175.55
## TIM2+I 58 -28486.84 57089.68 57536.61
## TIM2+G(4) 58 -28497.78 57111.57 57558.5
## TIM2+G(4)+I 59 -28484.09 57086.19 57540.82
## TIM3e 54 -29524.84 59157.68 59573.79
## TIM3e+I 55 -29250.44 58610.87 59034.68
## TIM3e+G(4) 55 -29257.81 58625.61 59049.42
## TIM3e+G(4)+I 56 -29245.88 58603.76 59035.28
## TIM3 57 -28819.5 57753.01 58192.23
## TIM3+I 58 -28486.66 57089.31 57536.24
## TIM3+G(4) 58 -28497.49 57110.98 57557.9
## TIM3+G(4)+I 59 -28483.72 57085.45 57540.08
## TVMe 55 -29529.65 59169.3 59593.11
## TVMe+I 56 -29261.4 58634.8 59066.31
## TVMe+G(4) 56 -29264.21 58640.42 59071.93
## TVMe+G(4)+I 57 -29254.95 58623.91 59063.13
## TVM 58 -28812.42 57740.84 58187.77
## TVM+I 59 -28485.21 57088.41 57543.04
## TVM+G(4) 59 -28495.91 57109.82 57564.46
## TVM+G(4)+I 60 -28482.36 57084.71 57547.05
## SYM 56 -29500.76 59113.52 59545.03
## SYM+I 57 -29236.87 58587.73 59026.96
## SYM+G(4) 57 -29244.37 58602.74 59041.97
## SYM+G(4)+I 58 -29232.61 58581.23 59028.16
## GTR 59 -28810.23 57738.45 58193.08
## GTR+I 60 -28485.15 57090.3 57552.64
## GTR+G(4) 60 -28495.91 57111.82 57574.15
## GTR+G(4)+I 61 -28482.35 57086.69 57556.74Trouver le meilleur modele
env <- attr(mySequences_gr_ext_3_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"mySequences_gr_ext_3_modelTest[order(mySequences_gr_ext_3_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 52 TPM3u+G(4)+I 58 -28483.74 57083.48 2.035756e-01 57083.90 2.040058e-01
## 44 TPM2u+G(4)+I 58 -28484.10 57084.21 1.416496e-01 57084.63 1.419490e-01
## 16 HKY+G(4)+I 57 -28485.21 57084.42 1.277156e-01 57084.82 1.288983e-01
## 84 TVM+G(4)+I 60 -28482.36 57084.71 1.100551e-01 57085.16 1.086910e-01
## 76 TIM3+G(4)+I 59 -28483.72 57085.45 7.633252e-02 57085.88 7.594279e-02
## 68 TIM2+G(4)+I 59 -28484.09 57086.19 5.264087e-02 57086.62 5.237210e-02
## 36 TPM1u+G(4)+I 58 -28485.18 57086.36 4.822142e-02 57086.78 4.832333e-02
## 24 TrN+G(4)+I 58 -28485.19 57086.38 4.795320e-02 57086.79 4.805454e-02
## 92 GTR+G(4)+I 61 -28482.35 57086.69 4.088827e-02 57087.16 4.008069e-02
## 50 TPM3u+I 57 -28486.73 57087.45 2.798709e-02 57087.86 2.824626e-02
## 42 TPM2u+I 57 -28486.89 57087.79 2.369086e-02 57088.19 2.391025e-02
## 14 HKY+I 56 -28488.10 57088.20 1.925343e-02 57088.59 1.956790e-02
## 60 TIM1+G(4)+I 59 -28485.16 57088.32 1.810362e-02 57088.76 1.801119e-02
## 82 TVM+I 59 -28485.21 57088.41 1.733062e-02 57088.84 1.724214e-02
## 74 TIM3+I 58 -28486.66 57089.31 1.103400e-02 57089.73 1.105732e-02
## 66 TIM2+I 58 -28486.84 57089.68 9.193478e-03 57090.10 9.212907e-03
## 22 TrN+I 57 -28488.03 57090.06 7.600912e-03 57090.46 7.671300e-03
## 34 TPM1u+I 57 -28488.08 57090.17 7.203964e-03 57090.57 7.270676e-03
## 90 GTR+I 60 -28485.15 57090.30 6.723302e-03 57090.75 6.639970e-03
## 58 TIM1+I 58 -28488.01 57092.03 2.843981e-03 57092.44 2.849991e-03
## 51 TPM3u+G(4) 57 -28497.50 57109.00 5.857448e-07 57109.41 5.911691e-07
## 43 TPM2u+G(4) 57 -28497.79 57109.58 4.391711e-07 57109.98 4.432380e-07
## 83 TVM+G(4) 59 -28495.91 57109.82 3.880581e-07 57110.26 3.860767e-07
## 15 HKY+G(4) 56 -28499.12 57110.24 3.148417e-07 57110.63 3.199841e-07
## 75 TIM3+G(4) 58 -28497.49 57110.98 2.182222e-07 57111.39 2.186833e-07
## 67 TIM2+G(4) 58 -28497.78 57111.57 1.622141e-07 57111.99 1.625569e-07
## 91 GTR+G(4) 60 -28495.91 57111.82 1.434459e-07 57112.26 1.416680e-07
## 35 TPM1u+G(4) 57 -28499.07 57112.14 1.218570e-07 57112.55 1.229854e-07
## 23 TrN+G(4) 57 -28499.11 57112.22 1.173580e-07 57112.62 1.184447e-07
## 59 TIM1+G(4) 58 -28499.06 57114.12 4.542330e-08 57114.53 4.551929e-08
## 65 TIM2 57 -28811.16 57736.33 3.513226e-143 57736.73 3.545760e-143
## 89 GTR 59 -28810.23 57738.45 1.214640e-143 57738.88 1.208438e-143
## 41 TPM2u 56 -28813.36 57738.72 1.063013e-143 57739.11 1.080376e-143
## 81 TVM 58 -28812.42 57740.84 3.670644e-144 57741.26 3.678401e-144
## 21 TrN 56 -28820.25 57752.49 1.086040e-146 57752.88 1.103779e-146
## 73 TIM3 57 -28819.50 57753.01 8.386723e-147 57753.41 8.464387e-147
## 57 TIM1 57 -28820.23 57754.47 4.037996e-147 57754.87 4.075389e-147
## 13 HKY 55 -28822.41 57754.82 3.384175e-147 57755.20 3.463127e-147
## 49 TPM3u 56 -28821.67 57755.34 2.613147e-147 57755.73 2.655828e-147
## 33 TPM1u 56 -28822.40 57756.80 1.259758e-147 57757.19 1.280334e-147
## 64 TIM2e+G(4)+I 56 -29234.19 58580.37 0.000000e+00 58580.77 0.000000e+00
## 88 SYM+G(4)+I 58 -29232.61 58581.23 0.000000e+00 58581.65 0.000000e+00
## 62 TIM2e+I 55 -29238.43 58586.86 0.000000e+00 58587.24 0.000000e+00
## 86 SYM+I 57 -29236.87 58587.73 0.000000e+00 58588.14 0.000000e+00
## 63 TIM2e+G(4) 55 -29245.96 58601.92 0.000000e+00 58602.30 0.000000e+00
## 87 SYM+G(4) 57 -29244.37 58602.74 0.000000e+00 58603.15 0.000000e+00
## 72 TIM3e+G(4)+I 56 -29245.88 58603.76 0.000000e+00 58604.15 0.000000e+00
## 20 TrNe+G(4)+I 55 -29247.28 58604.55 0.000000e+00 58604.93 0.000000e+00
## 56 TIM1e+G(4)+I 56 -29247.27 58606.54 0.000000e+00 58606.93 0.000000e+00
## 70 TIM3e+I 55 -29250.44 58610.87 0.000000e+00 58611.25 0.000000e+00
## 18 TrNe+I 54 -29251.79 58611.58 0.000000e+00 58611.94 0.000000e+00
## 54 TIM1e+I 55 -29251.77 58613.55 0.000000e+00 58613.92 0.000000e+00
## 40 TPM2+G(4)+I 55 -29256.56 58623.13 0.000000e+00 58623.50 0.000000e+00
## 80 TVMe+G(4)+I 57 -29254.95 58623.91 0.000000e+00 58624.31 0.000000e+00
## 71 TIM3e+G(4) 55 -29257.81 58625.61 0.000000e+00 58625.99 0.000000e+00
## 19 TrNe+G(4) 54 -29259.18 58626.36 0.000000e+00 58626.73 0.000000e+00
## 55 TIM1e+G(4) 55 -29259.18 58628.36 0.000000e+00 58628.73 0.000000e+00
## 38 TPM2+I 54 -29263.02 58634.04 0.000000e+00 58634.40 0.000000e+00
## 78 TVMe+I 56 -29261.40 58634.80 0.000000e+00 58635.19 0.000000e+00
## 39 TPM2+G(4) 54 -29265.82 58639.65 0.000000e+00 58640.01 0.000000e+00
## 79 TVMe+G(4) 56 -29264.21 58640.42 0.000000e+00 58640.81 0.000000e+00
## 48 TPM3+G(4)+I 55 -29267.19 58644.37 0.000000e+00 58644.75 0.000000e+00
## 12 K80+G(4)+I 54 -29268.61 58645.21 0.000000e+00 58645.58 0.000000e+00
## 28 TPM1+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 32 K81+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 46 TPM3+I 54 -29272.20 58652.39 0.000000e+00 58652.76 0.000000e+00
## 10 K80+I 53 -29273.48 58652.97 0.000000e+00 58653.32 0.000000e+00
## 26 TPM1+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 30 K81+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 47 TPM3+G(4) 54 -29276.93 58661.87 0.000000e+00 58662.23 0.000000e+00
## 11 K80+G(4) 53 -29278.31 58662.63 0.000000e+00 58662.98 0.000000e+00
## 27 TPM1+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 31 K81+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 61 TIM2e 54 -29501.48 59110.95 0.000000e+00 59111.31 0.000000e+00
## 85 SYM 56 -29500.76 59113.52 0.000000e+00 59113.91 0.000000e+00
## 17 TrNe 53 -29525.37 59156.74 0.000000e+00 59157.09 0.000000e+00
## 69 TIM3e 54 -29524.84 59157.68 0.000000e+00 59158.05 0.000000e+00
## 53 TIM1e 54 -29525.37 59158.74 0.000000e+00 59159.11 0.000000e+00
## 37 TPM2 53 -29530.37 59166.73 0.000000e+00 59167.08 0.000000e+00
## 77 TVMe 55 -29529.65 59169.30 0.000000e+00 59169.68 0.000000e+00
## 9 K80 52 -29553.92 59211.84 0.000000e+00 59212.18 0.000000e+00
## 45 TPM3 53 -29553.39 59212.79 0.000000e+00 59213.14 0.000000e+00
## 25 TPM1 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 29 K81 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 6 F81+I 55 -29596.55 59303.09 0.000000e+00 59303.47 0.000000e+00
## 8 F81+G(4)+I 56 -29596.04 59304.08 0.000000e+00 59304.47 0.000000e+00
## 7 F81+G(4) 55 -29609.53 59329.06 0.000000e+00 59329.44 0.000000e+00
## 5 F81 54 -29849.89 59807.78 0.000000e+00 59808.15 0.000000e+00
## 2 JC+I 52 -30308.99 60721.98 0.000000e+00 60722.32 0.000000e+00
## 4 JC+G(4)+I 53 -30308.43 60722.85 0.000000e+00 60723.20 0.000000e+00
## 3 JC+G(4) 52 -30321.38 60746.77 0.000000e+00 60747.10 0.000000e+00
## 1 JC 51 -30545.14 61192.28 0.000000e+00 61192.61 0.000000e+00
## BIC
## 52 57530.41
## 44 57531.14
## 16 57523.64
## 84 57547.05
## 76 57540.08
## 68 57540.82
## 36 57533.29
## 24 57533.30
## 92 57556.74
## 50 57526.67
## 42 57527.01
## 14 57519.72
## 60 57542.96
## 82 57543.04
## 74 57536.24
## 66 57536.61
## 22 57529.28
## 34 57529.39
## 90 57552.64
## 58 57538.95
## 51 57548.22
## 43 57548.80
## 83 57564.46
## 15 57541.76
## 75 57557.90
## 67 57558.50
## 91 57574.15
## 35 57551.36
## 23 57551.44
## 59 57561.04
## 65 58175.55
## 89 58193.08
## 41 58170.23
## 81 58187.77
## 21 58184.01
## 73 58192.23
## 57 58193.69
## 13 58178.63
## 49 58186.86
## 33 58188.31
## 64 59011.89
## 88 59028.16
## 62 59010.67
## 86 59026.96
## 63 59025.73
## 87 59041.97
## 72 59035.28
## 20 59028.36
## 56 59038.06
## 70 59034.68
## 18 59027.68
## 54 59037.36
## 40 59046.94
## 80 59063.13
## 71 59049.42
## 19 59042.47
## 55 59052.17
## 38 59050.14
## 78 59066.31
## 39 59055.75
## 79 59071.93
## 48 59068.18
## 12 59061.32
## 28 59071.02
## 32 59071.02
## 46 59068.50
## 10 59061.37
## 26 59071.03
## 30 59071.03
## 47 59077.97
## 11 59071.03
## 27 59080.72
## 31 59080.72
## 61 59527.06
## 85 59545.03
## 17 59565.14
## 69 59573.79
## 53 59574.85
## 37 59575.13
## 77 59593.11
## 9 59612.54
## 45 59621.19
## 25 59622.24
## 29 59622.24
## 6 59726.90
## 8 59735.60
## 7 59752.87
## 5 60223.89
## 2 61122.67
## 4 61131.25
## 3 61147.46
## 1 61585.27mySequences_gr_ext_3_modelTest[order(mySequences_gr_ext_3_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 14 HKY+I 56 -28488.10 57088.20 1.925343e-02 57088.59 1.956790e-02
## 16 HKY+G(4)+I 57 -28485.21 57084.42 1.277156e-01 57084.82 1.288983e-01
## 50 TPM3u+I 57 -28486.73 57087.45 2.798709e-02 57087.86 2.824626e-02
## 42 TPM2u+I 57 -28486.89 57087.79 2.369086e-02 57088.19 2.391025e-02
## 22 TrN+I 57 -28488.03 57090.06 7.600912e-03 57090.46 7.671300e-03
## 34 TPM1u+I 57 -28488.08 57090.17 7.203964e-03 57090.57 7.270676e-03
## 52 TPM3u+G(4)+I 58 -28483.74 57083.48 2.035756e-01 57083.90 2.040058e-01
## 44 TPM2u+G(4)+I 58 -28484.10 57084.21 1.416496e-01 57084.63 1.419490e-01
## 36 TPM1u+G(4)+I 58 -28485.18 57086.36 4.822142e-02 57086.78 4.832333e-02
## 24 TrN+G(4)+I 58 -28485.19 57086.38 4.795320e-02 57086.79 4.805454e-02
## 74 TIM3+I 58 -28486.66 57089.31 1.103400e-02 57089.73 1.105732e-02
## 66 TIM2+I 58 -28486.84 57089.68 9.193478e-03 57090.10 9.212907e-03
## 58 TIM1+I 58 -28488.01 57092.03 2.843981e-03 57092.44 2.849991e-03
## 76 TIM3+G(4)+I 59 -28483.72 57085.45 7.633252e-02 57085.88 7.594279e-02
## 68 TIM2+G(4)+I 59 -28484.09 57086.19 5.264087e-02 57086.62 5.237210e-02
## 15 HKY+G(4) 56 -28499.12 57110.24 3.148417e-07 57110.63 3.199841e-07
## 60 TIM1+G(4)+I 59 -28485.16 57088.32 1.810362e-02 57088.76 1.801119e-02
## 82 TVM+I 59 -28485.21 57088.41 1.733062e-02 57088.84 1.724214e-02
## 84 TVM+G(4)+I 60 -28482.36 57084.71 1.100551e-01 57085.16 1.086910e-01
## 51 TPM3u+G(4) 57 -28497.50 57109.00 5.857448e-07 57109.41 5.911691e-07
## 43 TPM2u+G(4) 57 -28497.79 57109.58 4.391711e-07 57109.98 4.432380e-07
## 35 TPM1u+G(4) 57 -28499.07 57112.14 1.218570e-07 57112.55 1.229854e-07
## 23 TrN+G(4) 57 -28499.11 57112.22 1.173580e-07 57112.62 1.184447e-07
## 90 GTR+I 60 -28485.15 57090.30 6.723302e-03 57090.75 6.639970e-03
## 92 GTR+G(4)+I 61 -28482.35 57086.69 4.088827e-02 57087.16 4.008069e-02
## 75 TIM3+G(4) 58 -28497.49 57110.98 2.182222e-07 57111.39 2.186833e-07
## 67 TIM2+G(4) 58 -28497.78 57111.57 1.622141e-07 57111.99 1.625569e-07
## 59 TIM1+G(4) 58 -28499.06 57114.12 4.542330e-08 57114.53 4.551929e-08
## 83 TVM+G(4) 59 -28495.91 57109.82 3.880581e-07 57110.26 3.860767e-07
## 91 GTR+G(4) 60 -28495.91 57111.82 1.434459e-07 57112.26 1.416680e-07
## 41 TPM2u 56 -28813.36 57738.72 1.063013e-143 57739.11 1.080376e-143
## 65 TIM2 57 -28811.16 57736.33 3.513226e-143 57736.73 3.545760e-143
## 13 HKY 55 -28822.41 57754.82 3.384175e-147 57755.20 3.463127e-147
## 21 TrN 56 -28820.25 57752.49 1.086040e-146 57752.88 1.103779e-146
## 49 TPM3u 56 -28821.67 57755.34 2.613147e-147 57755.73 2.655828e-147
## 81 TVM 58 -28812.42 57740.84 3.670644e-144 57741.26 3.678401e-144
## 33 TPM1u 56 -28822.40 57756.80 1.259758e-147 57757.19 1.280334e-147
## 73 TIM3 57 -28819.50 57753.01 8.386723e-147 57753.41 8.464387e-147
## 89 GTR 59 -28810.23 57738.45 1.214640e-143 57738.88 1.208438e-143
## 57 TIM1 57 -28820.23 57754.47 4.037996e-147 57754.87 4.075389e-147
## 62 TIM2e+I 55 -29238.43 58586.86 0.000000e+00 58587.24 0.000000e+00
## 64 TIM2e+G(4)+I 56 -29234.19 58580.37 0.000000e+00 58580.77 0.000000e+00
## 63 TIM2e+G(4) 55 -29245.96 58601.92 0.000000e+00 58602.30 0.000000e+00
## 86 SYM+I 57 -29236.87 58587.73 0.000000e+00 58588.14 0.000000e+00
## 18 TrNe+I 54 -29251.79 58611.58 0.000000e+00 58611.94 0.000000e+00
## 88 SYM+G(4)+I 58 -29232.61 58581.23 0.000000e+00 58581.65 0.000000e+00
## 20 TrNe+G(4)+I 55 -29247.28 58604.55 0.000000e+00 58604.93 0.000000e+00
## 70 TIM3e+I 55 -29250.44 58610.87 0.000000e+00 58611.25 0.000000e+00
## 72 TIM3e+G(4)+I 56 -29245.88 58603.76 0.000000e+00 58604.15 0.000000e+00
## 54 TIM1e+I 55 -29251.77 58613.55 0.000000e+00 58613.92 0.000000e+00
## 56 TIM1e+G(4)+I 56 -29247.27 58606.54 0.000000e+00 58606.93 0.000000e+00
## 87 SYM+G(4) 57 -29244.37 58602.74 0.000000e+00 58603.15 0.000000e+00
## 19 TrNe+G(4) 54 -29259.18 58626.36 0.000000e+00 58626.73 0.000000e+00
## 40 TPM2+G(4)+I 55 -29256.56 58623.13 0.000000e+00 58623.50 0.000000e+00
## 71 TIM3e+G(4) 55 -29257.81 58625.61 0.000000e+00 58625.99 0.000000e+00
## 38 TPM2+I 54 -29263.02 58634.04 0.000000e+00 58634.40 0.000000e+00
## 55 TIM1e+G(4) 55 -29259.18 58628.36 0.000000e+00 58628.73 0.000000e+00
## 39 TPM2+G(4) 54 -29265.82 58639.65 0.000000e+00 58640.01 0.000000e+00
## 12 K80+G(4)+I 54 -29268.61 58645.21 0.000000e+00 58645.58 0.000000e+00
## 10 K80+I 53 -29273.48 58652.97 0.000000e+00 58653.32 0.000000e+00
## 80 TVMe+G(4)+I 57 -29254.95 58623.91 0.000000e+00 58624.31 0.000000e+00
## 78 TVMe+I 56 -29261.40 58634.80 0.000000e+00 58635.19 0.000000e+00
## 48 TPM3+G(4)+I 55 -29267.19 58644.37 0.000000e+00 58644.75 0.000000e+00
## 46 TPM3+I 54 -29272.20 58652.39 0.000000e+00 58652.76 0.000000e+00
## 28 TPM1+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 32 K81+G(4)+I 55 -29268.60 58647.21 0.000000e+00 58647.58 0.000000e+00
## 26 TPM1+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 30 K81+I 54 -29273.46 58654.92 0.000000e+00 58655.28 0.000000e+00
## 11 K80+G(4) 53 -29278.31 58662.63 0.000000e+00 58662.98 0.000000e+00
## 79 TVMe+G(4) 56 -29264.21 58640.42 0.000000e+00 58640.81 0.000000e+00
## 47 TPM3+G(4) 54 -29276.93 58661.87 0.000000e+00 58662.23 0.000000e+00
## 27 TPM1+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 31 K81+G(4) 54 -29278.31 58664.62 0.000000e+00 58664.98 0.000000e+00
## 61 TIM2e 54 -29501.48 59110.95 0.000000e+00 59111.31 0.000000e+00
## 85 SYM 56 -29500.76 59113.52 0.000000e+00 59113.91 0.000000e+00
## 17 TrNe 53 -29525.37 59156.74 0.000000e+00 59157.09 0.000000e+00
## 69 TIM3e 54 -29524.84 59157.68 0.000000e+00 59158.05 0.000000e+00
## 53 TIM1e 54 -29525.37 59158.74 0.000000e+00 59159.11 0.000000e+00
## 37 TPM2 53 -29530.37 59166.73 0.000000e+00 59167.08 0.000000e+00
## 77 TVMe 55 -29529.65 59169.30 0.000000e+00 59169.68 0.000000e+00
## 9 K80 52 -29553.92 59211.84 0.000000e+00 59212.18 0.000000e+00
## 45 TPM3 53 -29553.39 59212.79 0.000000e+00 59213.14 0.000000e+00
## 25 TPM1 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 29 K81 53 -29553.92 59213.84 0.000000e+00 59214.19 0.000000e+00
## 6 F81+I 55 -29596.55 59303.09 0.000000e+00 59303.47 0.000000e+00
## 8 F81+G(4)+I 56 -29596.04 59304.08 0.000000e+00 59304.47 0.000000e+00
## 7 F81+G(4) 55 -29609.53 59329.06 0.000000e+00 59329.44 0.000000e+00
## 5 F81 54 -29849.89 59807.78 0.000000e+00 59808.15 0.000000e+00
## 2 JC+I 52 -30308.99 60721.98 0.000000e+00 60722.32 0.000000e+00
## 4 JC+G(4)+I 53 -30308.43 60722.85 0.000000e+00 60723.20 0.000000e+00
## 3 JC+G(4) 52 -30321.38 60746.77 0.000000e+00 60747.10 0.000000e+00
## 1 JC 51 -30545.14 61192.28 0.000000e+00 61192.61 0.000000e+00
## BIC
## 14 57519.72
## 16 57523.64
## 50 57526.67
## 42 57527.01
## 22 57529.28
## 34 57529.39
## 52 57530.41
## 44 57531.14
## 36 57533.29
## 24 57533.30
## 74 57536.24
## 66 57536.61
## 58 57538.95
## 76 57540.08
## 68 57540.82
## 15 57541.76
## 60 57542.96
## 82 57543.04
## 84 57547.05
## 51 57548.22
## 43 57548.80
## 35 57551.36
## 23 57551.44
## 90 57552.64
## 92 57556.74
## 75 57557.90
## 67 57558.50
## 59 57561.04
## 83 57564.46
## 91 57574.15
## 41 58170.23
## 65 58175.55
## 13 58178.63
## 21 58184.01
## 49 58186.86
## 81 58187.77
## 33 58188.31
## 73 58192.23
## 89 58193.08
## 57 58193.69
## 62 59010.67
## 64 59011.89
## 63 59025.73
## 86 59026.96
## 18 59027.68
## 88 59028.16
## 20 59028.36
## 70 59034.68
## 72 59035.28
## 54 59037.36
## 56 59038.06
## 87 59041.97
## 19 59042.47
## 40 59046.94
## 71 59049.42
## 38 59050.14
## 55 59052.17
## 39 59055.75
## 12 59061.32
## 10 59061.37
## 80 59063.13
## 78 59066.31
## 48 59068.18
## 46 59068.50
## 28 59071.02
## 32 59071.02
## 26 59071.03
## 30 59071.03
## 11 59071.03
## 79 59071.93
## 47 59077.97
## 27 59080.72
## 31 59080.72
## 61 59527.06
## 85 59545.03
## 17 59565.14
## 69 59573.79
## 53 59574.85
## 37 59575.13
## 77 59593.11
## 9 59612.54
## 45 59621.19
## 25 59622.24
## 29 59622.24
## 6 59726.90
## 8 59735.60
## 7 59752.87
## 5 60223.89
## 2 61122.67
## 4 61131.25
## 3 61147.46
## 1 61585.27Meilleur modele: HKY+G(4)+I
env$`HKY+G(4)+I`## pml(tree = `tree_HKY+G(4)+I`, data = data, bf = c(0.308803455371514,
## 0.278915306725343, 0.148686918077542, 0.263594319825602), Q = c(1,
## 23.8237170745377, 1, 1, 23.8237170745377, 1), model = "HKY",
## inv = 0.616439563626882, k = 4, shape = 5.42291970567487)Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_3 = dist.logDet(mySequences_align_gr_ext_3_phangorn) #HKY n'existe pas avec dist.ml()
# Construction arbre NJ
treeNJ_gr_ext_3 <- NJ(mySequences_align_gr_ext_3)
# Visualisation
plot(treeNJ_gr_ext_3, main="Arbre NJ Groupe externe 3")
Integration des parametres
fit_gr_ext_3 = pml(treeNJ_gr_ext_3, data=mySequences_align_gr_ext_3_phangorn)
fitHKY_gr_ext_3 <- update(fit_gr_ext_3, model="HKY", k=4, inv=0.616461296091301, shape=5.44888877718601)
fitHKY_gr_ext_3 <- optim.pml(fitHKY_gr_ext_3, model="HKY", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_gr_ext_3 = bootstrap.pml(fitHKY_gr_ext_3, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitHKY_gr_ext_3$tree), bs_gr_ext_3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
AA
Alignement
mySequences_align_aa_gr_ext_3 = AlignTranslation(Sequences_groupe_externe_3,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 6-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 1.14 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.12 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 1.84 secsConversion
mySequences_align_aa_gr_ext_3_ape = as.AAbin(mySequences_align_aa_gr_ext_3)
mySequences_align_aa_gr_ext_3_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_3_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Recherche du meilleur modele
mySequences_align_aa_gr_ext_3_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_3_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 51 -29557.62 59217.25 59571.94
## WAG+I 52 -29532.69 59169.38 59531.03
## WAG+G(4) 52 -29531.57 59167.14 59528.79
## WAG+G(4)+I 53 -29531.59 59169.18 59537.78
## JTT 51 -29442.65 58987.29 59341.98
## JTT+I 52 -29394.5 58893 59254.65
## JTT+G(4) 52 -29391.4 58886.8 59248.44
## JTT+G(4)+I 53 -29391.42 58888.84 59257.44
## LG 51 -29595.62 59293.24 59647.93
## LG+I 52 -29541.89 59187.79 59549.43
## LG+G(4) 52 -29534.56 59173.12 59534.76
## LG+G(4)+I 53 -29534.56 59175.13 59543.72
## Dayhoff 51 -30190.24 60482.49 60837.18
## Dayhoff+I 52 -30193.98 60491.95 60853.59
## Dayhoff+G(4) 52 -30194.67 60493.34 60854.99
## Dayhoff+G(4)+I 53 -30194.7 60495.4 60864
## cpREV 51 -29668.46 59438.91 59793.6
## cpREV+I 52 -29594.14 59292.28 59653.92
## cpREV+G(4) 52 -29594.87 59293.74 59655.39
## cpREV+G(4)+I 53 -29594.39 59294.78 59663.38
## mtmam 51 -30540.11 61182.22 61536.91
## mtmam+I 52 -30511.75 61127.5 61489.14
## mtmam+G(4) 52 -30514.09 61132.19 61493.83
## mtmam+G(4)+I 53 -30513.66 61133.32 61501.92
## mtArt 51 -29807.58 59717.15 60071.84
## mtArt+I 52 -29630.49 59364.98 59726.63
## mtArt+G(4) 52 -29587.87 59279.75 59641.39
## mtArt+G(4)+I 53 -29588.33 59282.67 59651.27
## MtZoa 51 -29742.34 59586.69 59941.38
## MtZoa+I 52 -29608.94 59321.88 59683.52
## MtZoa+G(4) 52 -29584 59272 59633.65
## MtZoa+G(4)+I 53 -29584.28 59274.56 59643.16
## mtREV24 51 -29258.64 58619.28 58973.97
## mtREV24+I 52 -29158.26 58420.51 58782.16
## mtREV24+G(4) 52 -29129 58362 58723.64
## mtREV24+G(4)+I 53 -29129.66 58365.32 58733.91
## VT 51 -29672.99 59447.98 59802.67
## VT+I 52 -29615.27 59334.54 59696.18
## VT+G(4) 52 -29595.31 59294.61 59656.26
## VT+G(4)+I 53 -29595.39 59296.79 59665.39
## RtREV 51 -29379.09 58860.18 59214.86
## RtREV+I 52 -29336.78 58777.56 59139.2
## RtREV+G(4) 52 -29331.3 58766.6 59128.24
## RtREV+G(4)+I 53 -29331.3 58768.61 59137.21
## HIVw 51 -30257.49 60616.98 60971.67
## HIVw+I 52 -30074.73 60253.45 60615.1
## HIVw+G(4) 52 -30052.63 60209.27 60570.91
## HIVw+G(4)+I 53 -30053.48 60212.96 60581.56
## HIVb 51 -29831.46 59764.91 60119.6
## HIVb+I 52 -29705.99 59515.97 59877.62
## HIVb+G(4) 52 -29701.24 59506.48 59868.12
## HIVb+G(4)+I 53 -29700.18 59506.37 59874.97
## FLU 51 -29409.51 58921.03 59275.71
## FLU+I 52 -29320.46 58744.93 59106.57
## FLU+G(4) 52 -30098.84 60301.69 60663.33
## FLU+G(4)+I 53 -30082.19 60270.38 60638.98
## Blosum62 51 -29596.14 59294.28 59648.97
## Blosum62+I 52 -29594.3 59292.61 59654.25
## Blosum62+G(4) 52 -29593.96 59291.92 59653.57
## Blosum62+G(4)+I 53 -29594 59294 59662.6
## Dayhoff_DCMut 51 -30186.65 60475.29 60829.98
## Dayhoff_DCMut+I 52 -30190.37 60484.74 60846.38
## Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 60847.79
## Dayhoff_DCMut+G(4)+I 53 -30191.1 60488.21 60856.8
## JTT_DCMut 51 -29459.26 59020.52 59375.21
## JTT_DCMut+I 52 -29411.19 58926.38 59288.02
## JTT_DCMut+G(4) 52 -29408.31 58920.62 59282.26
## JTT_DCMut+G(4)+I 53 -29408.33 58922.65 59291.25Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_3_modeltest, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"mySequences_align_aa_gr_ext_3_modeltest[order(mySequences_align_aa_gr_ext_3_modeltest$AIC), ]## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 52 -29129.00 58362.00 8.399080e-01 58362.72
## 36 mtREV24+G(4)+I 53 -29129.66 58365.32 1.600920e-01 58366.06
## 34 mtREV24+I 52 -29158.26 58420.51 1.654092e-13 58421.23
## 33 mtREV24 51 -29258.64 58619.28 1.139219e-56 58619.97
## 54 FLU+I 52 -29320.46 58744.93 5.925674e-84 58745.64
## 43 RtREV+G(4) 52 -29331.30 58766.60 1.167828e-88 58767.31
## 44 RtREV+G(4)+I 53 -29331.30 58768.61 4.270285e-89 58769.35
## 42 RtREV+I 52 -29336.78 58777.56 4.870374e-91 58778.27
## 41 RtREV 51 -29379.09 58860.18 5.581857e-109 58860.87
## 7 JTT+G(4) 52 -29391.40 58886.80 9.232021e-115 58887.52
## 8 JTT+G(4)+I 53 -29391.42 58888.84 3.334116e-115 58889.58
## 6 JTT+I 52 -29394.50 58893.00 4.152386e-116 58893.72
## 67 JTT_DCMut+G(4) 52 -29408.31 58920.62 4.187962e-122 58921.33
## 53 FLU 51 -29409.51 58921.03 3.415374e-122 58921.72
## 68 JTT_DCMut+G(4)+I 53 -29408.33 58922.65 1.512854e-122 58923.40
## 66 JTT_DCMut+I 52 -29411.19 58926.38 2.351608e-123 58927.09
## 5 JTT 51 -29442.65 58987.29 1.393959e-136 58987.98
## 65 JTT_DCMut 51 -29459.26 59020.52 8.472846e-144 59021.21
## 3 WAG+G(4) 52 -29531.57 59167.14 1.229597e-175 59167.86
## 4 WAG+G(4)+I 53 -29531.59 59169.18 4.436784e-176 59169.93
## 2 WAG+I 52 -29532.69 59169.38 4.008239e-176 59170.10
## 11 LG+G(4) 52 -29534.56 59173.12 6.187572e-177 59173.84
## 12 LG+G(4)+I 53 -29534.56 59175.13 2.272476e-177 59175.87
## 10 LG+I 52 -29541.89 59187.79 4.042479e-180 59188.51
## 1 WAG 51 -29557.62 59217.25 1.620749e-186 59217.94
## 31 MtZoa+G(4) 52 -29584.00 59272.00 2.088449e-198 59272.72
## 32 MtZoa+G(4)+I 53 -29584.28 59274.56 5.816963e-199 59275.30
## 27 mtArt+G(4) 52 -29587.87 59279.75 4.342329e-200 59280.47
## 28 mtArt+G(4)+I 53 -29588.33 59282.67 1.008501e-200 59283.41
## 59 Blosum62+G(4) 52 -29593.96 59291.92 9.868953e-203 59292.64
## 18 cpREV+I 52 -29594.14 59292.28 8.258313e-203 59293.00
## 58 Blosum62+I 52 -29594.30 59292.61 7.001220e-203 59293.33
## 9 LG 51 -29595.62 59293.24 5.109175e-203 59293.93
## 19 cpREV+G(4) 52 -29594.87 59293.74 3.967863e-203 59294.46
## 60 Blosum62+G(4)+I 53 -29594.00 59294.00 3.494117e-203 59294.74
## 57 Blosum62 51 -29596.14 59294.28 3.040701e-203 59294.97
## 39 VT+G(4) 52 -29595.31 59294.61 2.569882e-203 59295.33
## 20 cpREV+G(4)+I 53 -29594.39 59294.78 2.363334e-203 59295.53
## 40 VT+G(4)+I 53 -29595.39 59296.79 8.662865e-204 59297.53
## 30 MtZoa+I 52 -29608.94 59321.88 3.084856e-209 59322.60
## 38 VT+I 52 -29615.27 59334.54 5.501452e-212 59335.25
## 26 mtArt+I 52 -29630.49 59364.98 1.345919e-218 59365.70
## 17 cpREV 51 -29668.46 59438.91 1.190441e-234 59439.60
## 37 VT 51 -29672.99 59447.98 1.278323e-236 59448.67
## 52 HIVb+G(4)+I 53 -29700.18 59506.37 2.678299e-249 59507.11
## 51 HIVb+G(4) 52 -29701.24 59506.48 2.533576e-249 59507.20
## 50 HIVb+I 52 -29705.99 59515.97 2.199549e-251 59516.69
## 29 MtZoa 51 -29742.34 59586.69 9.690624e-267 59587.38
## 25 mtArt 51 -29807.58 59717.15 4.538413e-295 59717.84
## 49 HIVb 51 -29831.46 59764.91 1.930450e-305 59765.60
## 47 HIVw+G(4) 52 -30052.63 60209.27 0.000000e+00 60209.99
## 48 HIVw+G(4)+I 53 -30053.48 60212.96 0.000000e+00 60213.71
## 46 HIVw+I 52 -30074.73 60253.45 0.000000e+00 60254.17
## 56 FLU+G(4)+I 53 -30082.19 60270.38 0.000000e+00 60271.12
## 55 FLU+G(4) 52 -30098.84 60301.69 0.000000e+00 60302.40
## 61 Dayhoff_DCMut 51 -30186.65 60475.29 0.000000e+00 60475.98
## 13 Dayhoff 51 -30190.24 60482.49 0.000000e+00 60483.18
## 62 Dayhoff_DCMut+I 52 -30190.37 60484.74 0.000000e+00 60485.45
## 63 Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 0.000000e+00 60486.87
## 64 Dayhoff_DCMut+G(4)+I 53 -30191.10 60488.21 0.000000e+00 60488.95
## 14 Dayhoff+I 52 -30193.98 60491.95 0.000000e+00 60492.67
## 15 Dayhoff+G(4) 52 -30194.67 60493.34 0.000000e+00 60494.06
## 16 Dayhoff+G(4)+I 53 -30194.70 60495.40 0.000000e+00 60496.14
## 45 HIVw 51 -30257.49 60616.98 0.000000e+00 60617.67
## 22 mtmam+I 52 -30511.75 61127.50 0.000000e+00 61128.21
## 23 mtmam+G(4) 52 -30514.09 61132.19 0.000000e+00 61132.91
## 24 mtmam+G(4)+I 53 -30513.66 61133.32 0.000000e+00 61134.07
## 21 mtmam 51 -30540.11 61182.22 0.000000e+00 61182.91
## AICcw BIC
## 35 8.417590e-01 58723.64
## 36 1.582410e-01 58733.91
## 34 1.657737e-13 58782.16
## 33 1.157325e-56 58973.97
## 54 5.938732e-84 59106.57
## 43 1.170401e-88 59128.24
## 44 4.220911e-89 59137.21
## 42 4.881107e-91 59139.20
## 41 5.670572e-109 59214.86
## 7 9.252366e-115 59248.44
## 8 3.295567e-115 59257.44
## 6 4.161537e-116 59254.65
## 67 4.197191e-122 59282.26
## 53 3.469656e-122 59275.71
## 68 1.495362e-122 59291.25
## 66 2.356790e-123 59288.02
## 5 1.416114e-136 59341.98
## 65 8.607509e-144 59375.21
## 3 1.232307e-175 59528.79
## 4 4.385486e-176 59537.78
## 2 4.017072e-176 59531.03
## 11 6.201208e-177 59534.76
## 12 2.246201e-177 59543.72
## 10 4.051388e-180 59549.43
## 1 1.646509e-186 59571.94
## 31 2.093052e-198 59633.65
## 32 5.749707e-199 59643.16
## 27 4.351899e-200 59641.39
## 28 9.968407e-201 59651.27
## 59 9.890702e-203 59653.57
## 18 8.276513e-203 59653.92
## 58 7.016649e-203 59654.25
## 9 5.190378e-203 59647.93
## 19 3.976607e-203 59655.39
## 60 3.453718e-203 59662.60
## 57 3.089028e-203 59648.97
## 39 2.575546e-203 59656.26
## 20 2.336009e-203 59663.38
## 40 8.562705e-204 59665.39
## 30 3.091654e-209 59683.52
## 38 5.513576e-212 59696.18
## 26 1.348886e-218 59726.63
## 17 1.209361e-234 59793.60
## 37 1.298640e-236 59802.67
## 52 2.647332e-249 59874.97
## 51 2.539159e-249 59868.12
## 50 2.204396e-251 59877.62
## 29 9.844642e-267 59941.38
## 25 4.610544e-295 60071.84
## 49 1.961131e-305 60119.60
## 47 0.000000e+00 60570.91
## 48 0.000000e+00 60581.56
## 46 0.000000e+00 60615.10
## 56 0.000000e+00 60638.98
## 55 0.000000e+00 60663.33
## 61 0.000000e+00 60829.98
## 13 0.000000e+00 60837.18
## 62 0.000000e+00 60846.38
## 63 0.000000e+00 60847.79
## 64 0.000000e+00 60856.80
## 14 0.000000e+00 60853.59
## 15 0.000000e+00 60854.99
## 16 0.000000e+00 60864.00
## 45 0.000000e+00 60971.67
## 22 0.000000e+00 61489.14
## 23 0.000000e+00 61493.83
## 24 0.000000e+00 61501.92
## 21 0.000000e+00 61536.91mySequences_align_aa_gr_ext_3_modeltest[order(mySequences_align_aa_gr_ext_3_modeltest$BIC), ]## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 52 -29129.00 58362.00 8.399080e-01 58362.72
## 36 mtREV24+G(4)+I 53 -29129.66 58365.32 1.600920e-01 58366.06
## 34 mtREV24+I 52 -29158.26 58420.51 1.654092e-13 58421.23
## 33 mtREV24 51 -29258.64 58619.28 1.139219e-56 58619.97
## 54 FLU+I 52 -29320.46 58744.93 5.925674e-84 58745.64
## 43 RtREV+G(4) 52 -29331.30 58766.60 1.167828e-88 58767.31
## 44 RtREV+G(4)+I 53 -29331.30 58768.61 4.270285e-89 58769.35
## 42 RtREV+I 52 -29336.78 58777.56 4.870374e-91 58778.27
## 41 RtREV 51 -29379.09 58860.18 5.581857e-109 58860.87
## 7 JTT+G(4) 52 -29391.40 58886.80 9.232021e-115 58887.52
## 6 JTT+I 52 -29394.50 58893.00 4.152386e-116 58893.72
## 8 JTT+G(4)+I 53 -29391.42 58888.84 3.334116e-115 58889.58
## 53 FLU 51 -29409.51 58921.03 3.415374e-122 58921.72
## 67 JTT_DCMut+G(4) 52 -29408.31 58920.62 4.187962e-122 58921.33
## 66 JTT_DCMut+I 52 -29411.19 58926.38 2.351608e-123 58927.09
## 68 JTT_DCMut+G(4)+I 53 -29408.33 58922.65 1.512854e-122 58923.40
## 5 JTT 51 -29442.65 58987.29 1.393959e-136 58987.98
## 65 JTT_DCMut 51 -29459.26 59020.52 8.472846e-144 59021.21
## 3 WAG+G(4) 52 -29531.57 59167.14 1.229597e-175 59167.86
## 2 WAG+I 52 -29532.69 59169.38 4.008239e-176 59170.10
## 11 LG+G(4) 52 -29534.56 59173.12 6.187572e-177 59173.84
## 4 WAG+G(4)+I 53 -29531.59 59169.18 4.436784e-176 59169.93
## 12 LG+G(4)+I 53 -29534.56 59175.13 2.272476e-177 59175.87
## 10 LG+I 52 -29541.89 59187.79 4.042479e-180 59188.51
## 1 WAG 51 -29557.62 59217.25 1.620749e-186 59217.94
## 31 MtZoa+G(4) 52 -29584.00 59272.00 2.088449e-198 59272.72
## 27 mtArt+G(4) 52 -29587.87 59279.75 4.342329e-200 59280.47
## 32 MtZoa+G(4)+I 53 -29584.28 59274.56 5.816963e-199 59275.30
## 9 LG 51 -29595.62 59293.24 5.109175e-203 59293.93
## 57 Blosum62 51 -29596.14 59294.28 3.040701e-203 59294.97
## 28 mtArt+G(4)+I 53 -29588.33 59282.67 1.008501e-200 59283.41
## 59 Blosum62+G(4) 52 -29593.96 59291.92 9.868953e-203 59292.64
## 18 cpREV+I 52 -29594.14 59292.28 8.258313e-203 59293.00
## 58 Blosum62+I 52 -29594.30 59292.61 7.001220e-203 59293.33
## 19 cpREV+G(4) 52 -29594.87 59293.74 3.967863e-203 59294.46
## 39 VT+G(4) 52 -29595.31 59294.61 2.569882e-203 59295.33
## 60 Blosum62+G(4)+I 53 -29594.00 59294.00 3.494117e-203 59294.74
## 20 cpREV+G(4)+I 53 -29594.39 59294.78 2.363334e-203 59295.53
## 40 VT+G(4)+I 53 -29595.39 59296.79 8.662865e-204 59297.53
## 30 MtZoa+I 52 -29608.94 59321.88 3.084856e-209 59322.60
## 38 VT+I 52 -29615.27 59334.54 5.501452e-212 59335.25
## 26 mtArt+I 52 -29630.49 59364.98 1.345919e-218 59365.70
## 17 cpREV 51 -29668.46 59438.91 1.190441e-234 59439.60
## 37 VT 51 -29672.99 59447.98 1.278323e-236 59448.67
## 51 HIVb+G(4) 52 -29701.24 59506.48 2.533576e-249 59507.20
## 52 HIVb+G(4)+I 53 -29700.18 59506.37 2.678299e-249 59507.11
## 50 HIVb+I 52 -29705.99 59515.97 2.199549e-251 59516.69
## 29 MtZoa 51 -29742.34 59586.69 9.690624e-267 59587.38
## 25 mtArt 51 -29807.58 59717.15 4.538413e-295 59717.84
## 49 HIVb 51 -29831.46 59764.91 1.930450e-305 59765.60
## 47 HIVw+G(4) 52 -30052.63 60209.27 0.000000e+00 60209.99
## 48 HIVw+G(4)+I 53 -30053.48 60212.96 0.000000e+00 60213.71
## 46 HIVw+I 52 -30074.73 60253.45 0.000000e+00 60254.17
## 56 FLU+G(4)+I 53 -30082.19 60270.38 0.000000e+00 60271.12
## 55 FLU+G(4) 52 -30098.84 60301.69 0.000000e+00 60302.40
## 61 Dayhoff_DCMut 51 -30186.65 60475.29 0.000000e+00 60475.98
## 13 Dayhoff 51 -30190.24 60482.49 0.000000e+00 60483.18
## 62 Dayhoff_DCMut+I 52 -30190.37 60484.74 0.000000e+00 60485.45
## 63 Dayhoff_DCMut+G(4) 52 -30191.08 60486.15 0.000000e+00 60486.87
## 14 Dayhoff+I 52 -30193.98 60491.95 0.000000e+00 60492.67
## 15 Dayhoff+G(4) 52 -30194.67 60493.34 0.000000e+00 60494.06
## 64 Dayhoff_DCMut+G(4)+I 53 -30191.10 60488.21 0.000000e+00 60488.95
## 16 Dayhoff+G(4)+I 53 -30194.70 60495.40 0.000000e+00 60496.14
## 45 HIVw 51 -30257.49 60616.98 0.000000e+00 60617.67
## 22 mtmam+I 52 -30511.75 61127.50 0.000000e+00 61128.21
## 23 mtmam+G(4) 52 -30514.09 61132.19 0.000000e+00 61132.91
## 24 mtmam+G(4)+I 53 -30513.66 61133.32 0.000000e+00 61134.07
## 21 mtmam 51 -30540.11 61182.22 0.000000e+00 61182.91
## AICcw BIC
## 35 8.417590e-01 58723.64
## 36 1.582410e-01 58733.91
## 34 1.657737e-13 58782.16
## 33 1.157325e-56 58973.97
## 54 5.938732e-84 59106.57
## 43 1.170401e-88 59128.24
## 44 4.220911e-89 59137.21
## 42 4.881107e-91 59139.20
## 41 5.670572e-109 59214.86
## 7 9.252366e-115 59248.44
## 6 4.161537e-116 59254.65
## 8 3.295567e-115 59257.44
## 53 3.469656e-122 59275.71
## 67 4.197191e-122 59282.26
## 66 2.356790e-123 59288.02
## 68 1.495362e-122 59291.25
## 5 1.416114e-136 59341.98
## 65 8.607509e-144 59375.21
## 3 1.232307e-175 59528.79
## 2 4.017072e-176 59531.03
## 11 6.201208e-177 59534.76
## 4 4.385486e-176 59537.78
## 12 2.246201e-177 59543.72
## 10 4.051388e-180 59549.43
## 1 1.646509e-186 59571.94
## 31 2.093052e-198 59633.65
## 27 4.351899e-200 59641.39
## 32 5.749707e-199 59643.16
## 9 5.190378e-203 59647.93
## 57 3.089028e-203 59648.97
## 28 9.968407e-201 59651.27
## 59 9.890702e-203 59653.57
## 18 8.276513e-203 59653.92
## 58 7.016649e-203 59654.25
## 19 3.976607e-203 59655.39
## 39 2.575546e-203 59656.26
## 60 3.453718e-203 59662.60
## 20 2.336009e-203 59663.38
## 40 8.562705e-204 59665.39
## 30 3.091654e-209 59683.52
## 38 5.513576e-212 59696.18
## 26 1.348886e-218 59726.63
## 17 1.209361e-234 59793.60
## 37 1.298640e-236 59802.67
## 51 2.539159e-249 59868.12
## 52 2.647332e-249 59874.97
## 50 2.204396e-251 59877.62
## 29 9.844642e-267 59941.38
## 25 4.610544e-295 60071.84
## 49 1.961131e-305 60119.60
## 47 0.000000e+00 60570.91
## 48 0.000000e+00 60581.56
## 46 0.000000e+00 60615.10
## 56 0.000000e+00 60638.98
## 55 0.000000e+00 60663.33
## 61 0.000000e+00 60829.98
## 13 0.000000e+00 60837.18
## 62 0.000000e+00 60846.38
## 63 0.000000e+00 60847.79
## 14 0.000000e+00 60853.59
## 15 0.000000e+00 60854.99
## 64 0.000000e+00 60856.80
## 16 0.000000e+00 60864.00
## 45 0.000000e+00 60971.67
## 22 0.000000e+00 61489.14
## 23 0.000000e+00 61493.83
## 24 0.000000e+00 61501.92
## 21 0.000000e+00 61536.91Meilleur modele : mtREV24+G(4)
env$`mtREV24+G(4)`## pml(tree = `tree_mtREV24+G(4)`, data = data, model = "mtREV24",
## k = 4, shape = 0.568028964692472)Construction arbres
# Matrice de ditance
dm_aa_gr_ext_3 <- dist.ml(mySequences_align_aa_gr_ext_3_phangorn, model = "mtREV24")
# Construction arbre NJ
treeNJ_aa_gr_ext_3 <- NJ(dm_aa_gr_ext_3)Integration des parametres
fit_aa_gr_ext_3 = pml(treeNJ_aa_gr_ext_3, data=mySequences_align_aa_gr_ext_3_phangorn)
fitmtREV24_aa_gr_ext_3 <- update(fit_aa_gr_ext_3, model="mtREV24", shape =0.567580580902988, k = 4)
fitmtREV24_aa_gr_ext_3 <- optim.pml(fitmtREV24_aa_gr_ext_3, model="mtREV24", optGamma = TRUE, optShape = TRUE, rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_aa_gr_ext_3 = bootstrap.pml(fitmtREV24_aa_gr_ext_3, multicore=FALSE, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitmtREV24_aa_gr_ext_3$tree), bs_aa_gr_ext_3, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Tortue luth + Cistude
Code NCBI: - GQ152876.1 Dermochelys coriacea voucher - MW478028.1 Emys orbicularis voucher
Fusionner avec les cetaces
Sequences_groupe_externe_4 <- c(myNewSequences, myExterneSequences[7:8])ADN
Alignement
mySequences_align_gr_ext_4 = AlignSeqs(Sequences_groupe_externe_4, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 9-mers:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.08 secs
##
## Alignment converged - skipping remaining iteration.Recherche du meilleur modele
mySequences_align_gr_ext_4_ape = as.DNAbin(mySequences_align_gr_ext_4)
mySequences_align_gr_ext_4_phangorn = as.phyDat(mySequences_align_gr_ext_4_ape)
mySequences_gr_ext_4_modelTest = phangorn::modelTest(mySequences_align_gr_ext_4_phangorn)## Model df logLik AIC BIC
## JC 51 -4553.439 9208.877 9448.74
## JC+I 52 -4287.999 8679.998 8924.564
## JC+G(4) 52 -4291.647 8687.293 8931.859
## JC+G(4)+I 53 -4284.782 8675.565 8924.834
## F81 54 -4506.634 9121.268 9375.241
## F81+I 55 -4228.498 8566.996 8825.672
## F81+G(4) 55 -4230.284 8570.567 8829.243
## F81+G(4)+I 56 -4224.101 8560.203 8823.581
## K80 52 -4232.278 8568.555 8813.121
## K80+I 53 -3913.845 7933.691 8182.96
## K80+G(4) 53 -3907.147 7920.293 8169.562
## K80+G(4)+I 54 -3904.257 7916.514 8170.487
## HKY 55 -4183.735 8477.47 8736.146
## HKY+I 56 -3839.72 7791.44 8054.819
## HKY+G(4) 56 -3838.137 7788.274 8051.653
## HKY+G(4)+I 57 -3831.107 7776.215 8044.296
## TrNe 53 -4186.79 8479.579 8728.848
## TrNe+I 54 -3880.283 7868.566 8122.539
## TrNe+G(4) 54 -3881.555 7871.11 8125.083
## TrNe+G(4)+I 55 -3869.676 7849.352 8108.028
## TrN 56 -4164.857 8441.714 8705.093
## TrN+I 57 -3835.551 7785.102 8053.183
## TrN+G(4) 57 -3834.876 7783.753 8051.834
## TrN+G(4)+I 58 -3825.467 7766.934 8039.719
## TPM1 53 -4231.337 8568.674 8817.943
## TPM1+I 54 -3913.507 7935.014 8188.986
## TPM1+G(4) 54 -3906.704 7921.407 8175.38
## TPM1+G(4)+I 55 -3903.769 7917.538 8176.214
## K81 53 -4231.337 8568.674 8817.943
## K81+I 54 -3913.507 7935.014 8188.986
## K81+G(4) 54 -3906.704 7921.407 8175.38
## K81+G(4)+I 55 -3903.769 7917.538 8176.214
## TPM1u 56 -4183.048 8478.095 8741.474
## TPM1u+I 57 -3839.307 7792.613 8060.695
## TPM1u+G(4) 57 -3837.719 7789.439 8057.52
## TPM1u+G(4)+I 58 -3830.649 7777.297 8050.082
## TPM2 53 -4195.47 8496.94 8746.209
## TPM2+I 54 -3903.139 7914.278 8168.25
## TPM2+G(4) 54 -3895.221 7898.443 8152.415
## TPM2+G(4)+I 55 -3891.884 7893.767 8152.442
## TPM2u 56 -4158.175 8428.351 8691.729
## TPM2u+I 57 -3835.564 7785.128 8053.209
## TPM2u+G(4) 57 -3835.239 7784.479 8052.56
## TPM2u+G(4)+I 58 -3827.669 7771.338 8044.123
## TPM3 53 -4230.129 8566.257 8815.526
## TPM3+I 54 -3910.077 7928.153 8182.125
## TPM3+G(4) 54 -3902.727 7913.454 8167.426
## TPM3+G(4)+I 55 -3899.63 7909.261 8167.936
## TPM3u 56 -4182.147 8476.295 8739.673
## TPM3u+I 57 -3836.594 7787.187 8055.269
## TPM3u+G(4) 57 -3834.434 7782.869 8050.95
## TPM3u+G(4)+I 58 -3827.543 7771.087 8043.872
## TIM1e 54 -4185.808 8479.616 8733.589
## TIM1e+I 55 -3879.892 7869.783 8128.459
## TIM1e+G(4) 55 -3881.074 7872.148 8130.824
## TIM1e+G(4)+I 56 -3869.253 7850.507 8113.885
## TIM1 57 -4164.146 8442.291 8710.373
## TIM1+I 58 -3835.136 7786.272 8059.057
## TIM1+G(4) 58 -3834.458 7784.916 8057.701
## TIM1+G(4)+I 59 -3825.034 7768.067 8045.555
## TIM2e 54 -4149.681 8407.361 8661.334
## TIM2e+I 55 -3861.02 7832.041 8090.716
## TIM2e+G(4) 55 -3865.431 7840.861 8099.537
## TIM2e+G(4)+I 56 -3852.888 7817.775 8081.154
## TIM2 57 -4139.239 8392.478 8660.56
## TIM2+I 58 -3830.708 7777.417 8050.202
## TIM2+G(4) 58 -3831.158 7778.316 8051.101
## TIM2+G(4)+I 59 -3821.085 7760.169 8037.657
## TIM3e 54 -4184.626 8477.253 8731.225
## TIM3e+I 55 -3875.762 7861.524 8120.199
## TIM3e+G(4) 55 -3876.958 7863.916 8122.592
## TIM3e+G(4)+I 56 -3864.922 7841.845 8105.223
## TIM3 57 -4163.254 8440.508 8708.589
## TIM3+I 58 -3832.285 7780.571 8053.356
## TIM3+G(4) 58 -3831.138 7778.275 8051.06
## TIM3+G(4)+I 59 -3821.76 7761.52 8039.008
## TVMe 55 -4192.004 8494.008 8752.684
## TVMe+I 56 -3898.607 7909.215 8172.593
## TVMe+G(4) 56 -3889.857 7891.714 8155.092
## TVMe+G(4)+I 57 -3886.409 7886.818 8154.899
## TVM 58 -4155.419 8426.837 8699.622
## TVM+I 59 -3831.448 7780.897 8058.385
## TVM+G(4) 59 -3830.532 7779.063 8056.551
## TVM+G(4)+I 60 -3823.18 7766.36 8048.552
## SYM 56 -4146.395 8404.79 8668.169
## SYM+I 57 -3855.407 7824.813 8092.895
## SYM+G(4) 57 -3859.748 7833.496 8101.578
## SYM+G(4)+I 58 -3847.215 7810.431 8083.216
## GTR 59 -4136.615 8391.231 8668.719
## GTR+I 60 -3826.372 7772.745 8054.936
## GTR+G(4) 60 -3826.352 7772.704 8054.896
## GTR+G(4)+I 61 -3816.43 7754.86 8041.754Trouver le meilleur modele
env <- attr(mySequences_gr_ext_4_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"mySequences_gr_ext_4_modelTest[order(mySequences_gr_ext_4_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 92 GTR+G(4)+I 61 -3816.430 7754.860 8.977207e-01 7764.905 8.627364e-01
## 68 TIM2+G(4)+I 59 -3821.085 7760.169 6.312408e-02 7769.547 8.470607e-02
## 76 TIM3+G(4)+I 59 -3821.760 7761.520 3.212413e-02 7770.898 4.310730e-02
## 84 TVM+G(4)+I 60 -3823.180 7766.360 2.856606e-03 7776.068 3.249007e-03
## 24 TrN+G(4)+I 58 -3825.467 7766.934 2.144103e-03 7775.987 3.384116e-03
## 60 TIM1+G(4)+I 59 -3825.034 7768.067 1.216734e-03 7777.445 1.632733e-03
## 52 TPM3u+G(4)+I 58 -3827.543 7771.087 2.688408e-04 7780.140 4.243213e-04
## 44 TPM2u+G(4)+I 58 -3827.669 7771.338 2.370924e-04 7780.391 3.742117e-04
## 91 GTR+G(4) 60 -3826.352 7772.704 1.197383e-04 7782.413 1.361863e-04
## 90 GTR+I 60 -3826.372 7772.745 1.173496e-04 7782.453 1.334695e-04
## 16 HKY+G(4)+I 57 -3831.107 7776.215 2.070147e-05 7784.949 3.831312e-05
## 36 TPM1u+G(4)+I 58 -3830.649 7777.297 1.204718e-05 7786.350 1.901450e-05
## 66 TIM2+I 58 -3830.708 7777.417 1.134976e-05 7786.470 1.791374e-05
## 75 TIM3+G(4) 58 -3831.138 7778.275 7.387967e-06 7787.328 1.166070e-05
## 67 TIM2+G(4) 58 -3831.158 7778.316 7.238093e-06 7787.369 1.142415e-05
## 83 TVM+G(4) 59 -3830.532 7779.063 4.982555e-06 7788.441 6.686079e-06
## 74 TIM3+I 58 -3832.285 7780.571 2.344369e-06 7789.624 3.700204e-06
## 82 TVM+I 59 -3831.448 7780.897 1.992003e-06 7790.274 2.673064e-06
## 51 TPM3u+G(4) 57 -3834.434 7782.869 7.431360e-07 7791.603 1.375354e-06
## 23 TrN+G(4) 57 -3834.876 7783.753 4.776779e-07 7792.487 8.840594e-07
## 43 TPM2u+G(4) 57 -3835.239 7784.479 3.322764e-07 7793.213 6.149584e-07
## 59 TIM1+G(4) 58 -3834.458 7784.916 2.670098e-07 7793.969 4.214314e-07
## 22 TrN+I 57 -3835.551 7785.102 2.433380e-07 7793.836 4.503562e-07
## 42 TPM2u+I 57 -3835.564 7785.128 2.401904e-07 7793.862 4.445309e-07
## 58 TIM1+I 58 -3835.136 7786.272 1.355647e-07 7795.325 2.139667e-07
## 50 TPM3u+I 57 -3836.594 7787.187 8.576882e-08 7795.922 1.587361e-07
## 15 HKY+G(4) 56 -3838.137 7788.274 4.981261e-08 7796.696 1.077715e-07
## 35 TPM1u+G(4) 57 -3837.719 7789.439 2.782580e-08 7798.173 5.149843e-08
## 14 HKY+I 56 -3839.720 7791.440 1.022806e-08 7799.862 2.212880e-08
## 34 TPM1u+I 57 -3839.307 7792.613 5.689277e-09 7801.348 1.052939e-08
## 88 SYM+G(4)+I 58 -3847.215 7810.431 7.691932e-13 7819.484 1.214046e-12
## 64 TIM2e+G(4)+I 56 -3852.888 7817.775 1.955508e-14 7826.197 4.230816e-14
## 86 SYM+I 57 -3855.407 7824.813 5.793534e-16 7833.548 1.072235e-15
## 62 TIM2e+I 55 -3861.020 7832.041 1.561429e-17 7840.157 3.937150e-17
## 87 SYM+G(4) 57 -3859.748 7833.496 7.542169e-18 7842.230 1.395862e-17
## 63 TIM2e+G(4) 55 -3865.431 7840.861 1.897184e-19 7848.977 4.783757e-19
## 72 TIM3e+G(4)+I 56 -3864.922 7841.845 1.160361e-19 7850.267 2.510485e-19
## 20 TrNe+G(4)+I 55 -3869.676 7849.352 2.718452e-21 7857.468 6.854589e-21
## 56 TIM1e+G(4)+I 56 -3869.253 7850.507 1.526387e-21 7858.929 3.302396e-21
## 70 TIM3e+I 55 -3875.762 7861.524 6.185701e-24 7869.640 1.559727e-23
## 71 TIM3e+G(4) 55 -3876.958 7863.916 1.869915e-24 7872.032 4.714998e-24
## 18 TrNe+I 54 -3880.283 7868.566 1.828357e-25 7876.382 5.356709e-25
## 54 TIM1e+I 55 -3879.892 7869.783 9.949979e-26 7877.899 2.508892e-25
## 19 TrNe+G(4) 54 -3881.555 7871.110 5.124203e-26 7878.926 1.501286e-25
## 55 TIM1e+G(4) 55 -3881.074 7872.148 3.049738e-26 7880.264 7.689927e-26
## 80 TVMe+G(4)+I 57 -3886.409 7886.818 1.990083e-29 7895.552 3.683133e-29
## 79 TVMe+G(4) 56 -3889.857 7891.714 1.720772e-30 7900.136 3.722955e-30
## 40 TPM2+G(4)+I 55 -3891.884 7893.767 6.163194e-31 7901.883 1.554052e-30
## 39 TPM2+G(4) 54 -3895.221 7898.443 5.949627e-32 7906.259 1.743118e-31
## 78 TVMe+I 56 -3898.607 7909.215 2.725193e-34 7917.637 5.896060e-34
## 48 TPM3+G(4)+I 55 -3899.630 7909.261 2.662870e-34 7917.377 6.714439e-34
## 47 TPM3+G(4) 54 -3902.727 7913.454 3.272598e-35 7921.270 9.588037e-35
## 38 TPM2+I 54 -3903.139 7914.278 2.167729e-35 7922.093 6.350998e-35
## 12 K80+G(4)+I 54 -3904.257 7916.514 7.084052e-36 7924.330 2.075481e-35
## 28 TPM1+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 32 K81+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 11 K80+G(4) 53 -3907.147 7920.293 1.070896e-36 7927.815 3.634535e-36
## 27 TPM1+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 31 K81+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 46 TPM3+I 54 -3910.077 7928.153 2.103725e-38 7935.969 6.163481e-38
## 10 K80+I 53 -3913.845 7933.691 1.319691e-39 7941.212 4.478927e-39
## 26 TPM1+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 30 K81+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 89 GTR 59 -4136.615 8391.231 5.847519e-139 8400.608 7.846774e-139
## 65 TIM2 57 -4139.239 8392.478 3.133793e-139 8401.213 5.799848e-139
## 85 SYM 56 -4146.395 8404.790 6.644955e-142 8413.213 1.437661e-141
## 61 TIM2e 54 -4149.681 8407.361 1.837467e-142 8415.177 5.383397e-142
## 81 TVM 58 -4155.419 8426.837 1.084222e-146 8435.890 1.711267e-146
## 41 TPM2u 56 -4158.175 8428.351 5.086543e-147 8436.773 1.100493e-146
## 73 TIM3 57 -4163.254 8440.508 1.165653e-149 8449.242 2.157326e-149
## 21 TrN 56 -4164.857 8441.714 6.377326e-150 8450.136 1.379759e-149
## 57 TIM1 57 -4164.146 8442.291 4.778564e-150 8451.026 8.843897e-150
## 49 TPM3u 56 -4182.147 8476.295 1.974906e-157 8484.717 4.272785e-157
## 69 TIM3e 54 -4184.626 8477.253 1.223344e-157 8485.068 3.584146e-157
## 13 HKY 55 -4183.735 8477.470 1.097208e-157 8485.586 2.766613e-157
## 33 TPM1u 56 -4183.048 8478.095 8.027521e-158 8486.517 1.736785e-157
## 17 TrNe 53 -4186.790 8479.579 3.822214e-158 8487.101 1.297229e-157
## 53 TIM1e 54 -4185.808 8479.616 3.751717e-158 8487.432 1.099175e-157
## 77 TVMe 55 -4192.004 8494.008 2.812296e-161 8502.124 7.091215e-161
## 37 TPM2 53 -4195.470 8496.940 6.491684e-162 8504.462 2.203226e-161
## 8 F81+G(4)+I 56 -4224.101 8560.203 1.188832e-175 8568.625 2.572083e-175
## 45 TPM3 53 -4230.129 8566.257 5.760596e-177 8573.779 1.955100e-176
## 6 F81+I 55 -4228.498 8566.996 3.980571e-177 8575.112 1.003703e-176
## 9 K80 52 -4232.278 8568.555 1.825468e-177 8575.789 7.155385e-177
## 25 TPM1 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 29 K81 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 7 F81+G(4) 55 -4230.284 8570.567 6.675493e-178 8578.683 1.683228e-177
## 4 JC+G(4)+I 53 -4284.782 8675.565 1.058262e-200 8683.086 3.591657e-200
## 2 JC+I 52 -4287.999 8679.998 1.153410e-201 8687.231 4.521083e-201
## 3 JC+G(4) 52 -4291.647 8687.293 3.004938e-203 8694.527 1.177862e-202
## 5 F81 54 -4506.634 9121.268 1.742945e-297 9129.084 5.106470e-297
## 1 JC 51 -4553.439 9208.877 1.649059e-316 9215.829 7.443029e-316
## BIC
## 92 8041.754
## 68 8037.657
## 76 8039.008
## 84 8048.552
## 24 8039.719
## 60 8045.555
## 52 8043.872
## 44 8044.123
## 91 8054.896
## 90 8054.936
## 16 8044.296
## 36 8050.082
## 66 8050.202
## 75 8051.060
## 67 8051.101
## 83 8056.551
## 74 8053.356
## 82 8058.385
## 51 8050.950
## 23 8051.834
## 43 8052.560
## 59 8057.701
## 22 8053.183
## 42 8053.209
## 58 8059.057
## 50 8055.269
## 15 8051.653
## 35 8057.520
## 14 8054.819
## 34 8060.695
## 88 8083.216
## 64 8081.154
## 86 8092.895
## 62 8090.716
## 87 8101.578
## 63 8099.537
## 72 8105.223
## 20 8108.028
## 56 8113.885
## 70 8120.199
## 71 8122.592
## 18 8122.539
## 54 8128.459
## 19 8125.083
## 55 8130.824
## 80 8154.899
## 79 8155.092
## 40 8152.442
## 39 8152.415
## 78 8172.593
## 48 8167.936
## 47 8167.426
## 38 8168.250
## 12 8170.487
## 28 8176.214
## 32 8176.214
## 11 8169.562
## 27 8175.380
## 31 8175.380
## 46 8182.125
## 10 8182.960
## 26 8188.986
## 30 8188.986
## 89 8668.719
## 65 8660.560
## 85 8668.169
## 61 8661.334
## 81 8699.622
## 41 8691.729
## 73 8708.589
## 21 8705.093
## 57 8710.373
## 49 8739.673
## 69 8731.225
## 13 8736.146
## 33 8741.474
## 17 8728.848
## 53 8733.589
## 77 8752.684
## 37 8746.209
## 8 8823.581
## 45 8815.526
## 6 8825.672
## 9 8813.121
## 25 8817.943
## 29 8817.943
## 7 8829.243
## 4 8924.834
## 2 8924.564
## 3 8931.859
## 5 9375.241
## 1 9448.740mySequences_gr_ext_4_modelTest[order(mySequences_gr_ext_4_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 68 TIM2+G(4)+I 59 -3821.085 7760.169 6.312408e-02 7769.547 8.470607e-02
## 76 TIM3+G(4)+I 59 -3821.760 7761.520 3.212413e-02 7770.898 4.310730e-02
## 24 TrN+G(4)+I 58 -3825.467 7766.934 2.144103e-03 7775.987 3.384116e-03
## 92 GTR+G(4)+I 61 -3816.430 7754.860 8.977207e-01 7764.905 8.627364e-01
## 52 TPM3u+G(4)+I 58 -3827.543 7771.087 2.688408e-04 7780.140 4.243213e-04
## 44 TPM2u+G(4)+I 58 -3827.669 7771.338 2.370924e-04 7780.391 3.742117e-04
## 16 HKY+G(4)+I 57 -3831.107 7776.215 2.070147e-05 7784.949 3.831312e-05
## 60 TIM1+G(4)+I 59 -3825.034 7768.067 1.216734e-03 7777.445 1.632733e-03
## 84 TVM+G(4)+I 60 -3823.180 7766.360 2.856606e-03 7776.068 3.249007e-03
## 36 TPM1u+G(4)+I 58 -3830.649 7777.297 1.204718e-05 7786.350 1.901450e-05
## 66 TIM2+I 58 -3830.708 7777.417 1.134976e-05 7786.470 1.791374e-05
## 51 TPM3u+G(4) 57 -3834.434 7782.869 7.431360e-07 7791.603 1.375354e-06
## 75 TIM3+G(4) 58 -3831.138 7778.275 7.387967e-06 7787.328 1.166070e-05
## 67 TIM2+G(4) 58 -3831.158 7778.316 7.238093e-06 7787.369 1.142415e-05
## 15 HKY+G(4) 56 -3838.137 7788.274 4.981261e-08 7796.696 1.077715e-07
## 23 TrN+G(4) 57 -3834.876 7783.753 4.776779e-07 7792.487 8.840594e-07
## 43 TPM2u+G(4) 57 -3835.239 7784.479 3.322764e-07 7793.213 6.149584e-07
## 22 TrN+I 57 -3835.551 7785.102 2.433380e-07 7793.836 4.503562e-07
## 42 TPM2u+I 57 -3835.564 7785.128 2.401904e-07 7793.862 4.445309e-07
## 74 TIM3+I 58 -3832.285 7780.571 2.344369e-06 7789.624 3.700204e-06
## 14 HKY+I 56 -3839.720 7791.440 1.022806e-08 7799.862 2.212880e-08
## 91 GTR+G(4) 60 -3826.352 7772.704 1.197383e-04 7782.413 1.361863e-04
## 90 GTR+I 60 -3826.372 7772.745 1.173496e-04 7782.453 1.334695e-04
## 50 TPM3u+I 57 -3836.594 7787.187 8.576882e-08 7795.922 1.587361e-07
## 83 TVM+G(4) 59 -3830.532 7779.063 4.982555e-06 7788.441 6.686079e-06
## 35 TPM1u+G(4) 57 -3837.719 7789.439 2.782580e-08 7798.173 5.149843e-08
## 59 TIM1+G(4) 58 -3834.458 7784.916 2.670098e-07 7793.969 4.214314e-07
## 82 TVM+I 59 -3831.448 7780.897 1.992003e-06 7790.274 2.673064e-06
## 58 TIM1+I 58 -3835.136 7786.272 1.355647e-07 7795.325 2.139667e-07
## 34 TPM1u+I 57 -3839.307 7792.613 5.689277e-09 7801.348 1.052939e-08
## 64 TIM2e+G(4)+I 56 -3852.888 7817.775 1.955508e-14 7826.197 4.230816e-14
## 88 SYM+G(4)+I 58 -3847.215 7810.431 7.691932e-13 7819.484 1.214046e-12
## 62 TIM2e+I 55 -3861.020 7832.041 1.561429e-17 7840.157 3.937150e-17
## 86 SYM+I 57 -3855.407 7824.813 5.793534e-16 7833.548 1.072235e-15
## 63 TIM2e+G(4) 55 -3865.431 7840.861 1.897184e-19 7848.977 4.783757e-19
## 87 SYM+G(4) 57 -3859.748 7833.496 7.542169e-18 7842.230 1.395862e-17
## 72 TIM3e+G(4)+I 56 -3864.922 7841.845 1.160361e-19 7850.267 2.510485e-19
## 20 TrNe+G(4)+I 55 -3869.676 7849.352 2.718452e-21 7857.468 6.854589e-21
## 56 TIM1e+G(4)+I 56 -3869.253 7850.507 1.526387e-21 7858.929 3.302396e-21
## 70 TIM3e+I 55 -3875.762 7861.524 6.185701e-24 7869.640 1.559727e-23
## 18 TrNe+I 54 -3880.283 7868.566 1.828357e-25 7876.382 5.356709e-25
## 71 TIM3e+G(4) 55 -3876.958 7863.916 1.869915e-24 7872.032 4.714998e-24
## 19 TrNe+G(4) 54 -3881.555 7871.110 5.124203e-26 7878.926 1.501286e-25
## 54 TIM1e+I 55 -3879.892 7869.783 9.949979e-26 7877.899 2.508892e-25
## 55 TIM1e+G(4) 55 -3881.074 7872.148 3.049738e-26 7880.264 7.689927e-26
## 39 TPM2+G(4) 54 -3895.221 7898.443 5.949627e-32 7906.259 1.743118e-31
## 40 TPM2+G(4)+I 55 -3891.884 7893.767 6.163194e-31 7901.883 1.554052e-30
## 80 TVMe+G(4)+I 57 -3886.409 7886.818 1.990083e-29 7895.552 3.683133e-29
## 79 TVMe+G(4) 56 -3889.857 7891.714 1.720772e-30 7900.136 3.722955e-30
## 47 TPM3+G(4) 54 -3902.727 7913.454 3.272598e-35 7921.270 9.588037e-35
## 48 TPM3+G(4)+I 55 -3899.630 7909.261 2.662870e-34 7917.377 6.714439e-34
## 38 TPM2+I 54 -3903.139 7914.278 2.167729e-35 7922.093 6.350998e-35
## 11 K80+G(4) 53 -3907.147 7920.293 1.070896e-36 7927.815 3.634535e-36
## 12 K80+G(4)+I 54 -3904.257 7916.514 7.084052e-36 7924.330 2.075481e-35
## 78 TVMe+I 56 -3898.607 7909.215 2.725193e-34 7917.637 5.896060e-34
## 27 TPM1+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 31 K81+G(4) 54 -3906.704 7921.407 6.134263e-37 7929.223 1.797212e-36
## 28 TPM1+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 32 K81+G(4)+I 55 -3903.769 7917.538 4.245940e-36 7925.654 1.070616e-35
## 46 TPM3+I 54 -3910.077 7928.153 2.103725e-38 7935.969 6.163481e-38
## 10 K80+I 53 -3913.845 7933.691 1.319691e-39 7941.212 4.478927e-39
## 26 TPM1+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 30 K81+I 54 -3913.507 7935.014 6.809666e-40 7942.830 1.995091e-39
## 65 TIM2 57 -4139.239 8392.478 3.133793e-139 8401.213 5.799848e-139
## 61 TIM2e 54 -4149.681 8407.361 1.837467e-142 8415.177 5.383397e-142
## 85 SYM 56 -4146.395 8404.790 6.644955e-142 8413.213 1.437661e-141
## 89 GTR 59 -4136.615 8391.231 5.847519e-139 8400.608 7.846774e-139
## 41 TPM2u 56 -4158.175 8428.351 5.086543e-147 8436.773 1.100493e-146
## 81 TVM 58 -4155.419 8426.837 1.084222e-146 8435.890 1.711267e-146
## 21 TrN 56 -4164.857 8441.714 6.377326e-150 8450.136 1.379759e-149
## 73 TIM3 57 -4163.254 8440.508 1.165653e-149 8449.242 2.157326e-149
## 57 TIM1 57 -4164.146 8442.291 4.778564e-150 8451.026 8.843897e-150
## 17 TrNe 53 -4186.790 8479.579 3.822214e-158 8487.101 1.297229e-157
## 69 TIM3e 54 -4184.626 8477.253 1.223344e-157 8485.068 3.584146e-157
## 53 TIM1e 54 -4185.808 8479.616 3.751717e-158 8487.432 1.099175e-157
## 13 HKY 55 -4183.735 8477.470 1.097208e-157 8485.586 2.766613e-157
## 49 TPM3u 56 -4182.147 8476.295 1.974906e-157 8484.717 4.272785e-157
## 33 TPM1u 56 -4183.048 8478.095 8.027521e-158 8486.517 1.736785e-157
## 37 TPM2 53 -4195.470 8496.940 6.491684e-162 8504.462 2.203226e-161
## 77 TVMe 55 -4192.004 8494.008 2.812296e-161 8502.124 7.091215e-161
## 9 K80 52 -4232.278 8568.555 1.825468e-177 8575.789 7.155385e-177
## 45 TPM3 53 -4230.129 8566.257 5.760596e-177 8573.779 1.955100e-176
## 25 TPM1 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 29 K81 53 -4231.337 8568.674 1.720170e-177 8576.196 5.838120e-177
## 8 F81+G(4)+I 56 -4224.101 8560.203 1.188832e-175 8568.625 2.572083e-175
## 6 F81+I 55 -4228.498 8566.996 3.980571e-177 8575.112 1.003703e-176
## 7 F81+G(4) 55 -4230.284 8570.567 6.675493e-178 8578.683 1.683228e-177
## 2 JC+I 52 -4287.999 8679.998 1.153410e-201 8687.231 4.521083e-201
## 4 JC+G(4)+I 53 -4284.782 8675.565 1.058262e-200 8683.086 3.591657e-200
## 3 JC+G(4) 52 -4291.647 8687.293 3.004938e-203 8694.527 1.177862e-202
## 5 F81 54 -4506.634 9121.268 1.742945e-297 9129.084 5.106470e-297
## 1 JC 51 -4553.439 9208.877 1.649059e-316 9215.829 7.443029e-316
## BIC
## 68 8037.657
## 76 8039.008
## 24 8039.719
## 92 8041.754
## 52 8043.872
## 44 8044.123
## 16 8044.296
## 60 8045.555
## 84 8048.552
## 36 8050.082
## 66 8050.202
## 51 8050.950
## 75 8051.060
## 67 8051.101
## 15 8051.653
## 23 8051.834
## 43 8052.560
## 22 8053.183
## 42 8053.209
## 74 8053.356
## 14 8054.819
## 91 8054.896
## 90 8054.936
## 50 8055.269
## 83 8056.551
## 35 8057.520
## 59 8057.701
## 82 8058.385
## 58 8059.057
## 34 8060.695
## 64 8081.154
## 88 8083.216
## 62 8090.716
## 86 8092.895
## 63 8099.537
## 87 8101.578
## 72 8105.223
## 20 8108.028
## 56 8113.885
## 70 8120.199
## 18 8122.539
## 71 8122.592
## 19 8125.083
## 54 8128.459
## 55 8130.824
## 39 8152.415
## 40 8152.442
## 80 8154.899
## 79 8155.092
## 47 8167.426
## 48 8167.936
## 38 8168.250
## 11 8169.562
## 12 8170.487
## 78 8172.593
## 27 8175.380
## 31 8175.380
## 28 8176.214
## 32 8176.214
## 46 8182.125
## 10 8182.960
## 26 8188.986
## 30 8188.986
## 65 8660.560
## 61 8661.334
## 85 8668.169
## 89 8668.719
## 41 8691.729
## 81 8699.622
## 21 8705.093
## 73 8708.589
## 57 8710.373
## 17 8728.848
## 69 8731.225
## 53 8733.589
## 13 8736.146
## 49 8739.673
## 33 8741.474
## 37 8746.209
## 77 8752.684
## 9 8813.121
## 45 8815.526
## 25 8817.943
## 29 8817.943
## 8 8823.581
## 6 8825.672
## 7 8829.243
## 2 8924.564
## 4 8924.834
## 3 8931.859
## 5 9375.241
## 1 9448.740Meilleur modele: TIM2+G(4)+I
env$`TIM2+G(4)+I`## pml(tree = `tree_TIM2+G(4)+I`, data = data, bf = c(0.271785050414015,
## 0.266095871120374, 0.168140595955613, 0.293978482509998), Q = c(3.37736920870854,
## 31.3229227038796, 3.37736920870854, 1, 56.2297502116579, 1),
## model = "TIM2", inv = 0.572671397044045, k = 4, shape = 2.48833057131467)Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_4 = dist.logDet(mySequences_align_gr_ext_4_phangorn)
# Construction arbre NJ
treeNJ_gr_ext_4 <- NJ(mySequences_align_gr_ext_4)
# Visualisation
plot(treeNJ_gr_ext_4, main="Arbre NJ Groupe externe 4")
Integration des parametres
fit_gr_ext_4 = pml(treeNJ_gr_ext_4, data=mySequences_align_gr_ext_4_phangorn)
fitTIM2_gr_ext_4 <- update(fit_gr_ext_4, model="TIM2", k=4, inv=0.572669834174348, shape=2.4882559444008)
fitTIM2_gr_ext_4 <- optim.pml(fitTIM2_gr_ext_4, model="TIM2", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_gr_ext_4 = bootstrap.pml(fitTIM2_gr_ext_4, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTIM2_gr_ext_4$tree), bs_gr_ext_4, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
AA
Alignement
mySequences_align_aa_gr_ext_4 = AlignTranslation(Sequences_groupe_externe_4,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 5-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.11 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.05 secs
##
## Alignment converged - skipping remaining iteration.Conversion
mySequences_align_aa_gr_ext_4_ape = as.AAbin(mySequences_align_aa_gr_ext_4)
mySequences_align_aa_gr_ext_4_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_4_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Recherche du meilleur modele
mySequences_align_aa_gr_ext_4_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_4_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 51 -989.4844 2080.969 2263.919
## WAG+I 52 -978.0493 2060.099 2246.636
## WAG+G(4) 52 -979.044 2062.088 2248.625
## WAG+G(4)+I 53 -978.0852 2062.17 2252.295
## JTT 51 -985.0266 2072.053 2255.003
## JTT+I 52 -973.9716 2051.943 2238.48
## JTT+G(4) 52 -974.8447 2053.689 2240.226
## JTT+G(4)+I 53 -974.0697 2054.139 2244.263
## LG 51 -986.8872 2075.774 2258.724
## LG+I 52 -976.374 2056.748 2243.285
## LG+G(4) 52 -977.0353 2058.071 2244.607
## LG+G(4)+I 53 -976.3983 2058.797 2248.921
## Dayhoff 51 -1000.945 2103.889 2286.839
## Dayhoff+I 52 -989.3875 2082.775 2269.312
## Dayhoff+G(4) 52 -990.3689 2084.738 2271.275
## Dayhoff+G(4)+I 53 -989.579 2085.158 2275.282
## cpREV 51 -975.0217 2052.043 2234.993
## cpREV+I 52 -963.9911 2031.982 2218.519
## cpREV+G(4) 52 -964.818 2033.636 2220.173
## cpREV+G(4)+I 53 -964.1154 2034.231 2224.355
## mtmam 51 -945.8698 1993.74 2176.689
## mtmam+I 52 -936.5416 1977.083 2163.62## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive
## Warning in optimize(f = fn, interval = c(0.1, 100), lower = 0.1, upper = 100, :
## NA / Inf remplacé par la valeur maximale positive## mtmam+G(4) 52 -936.6824 1977.365 2163.902
## mtmam+G(4)+I 53 -936.5512 1979.102 2169.227
## mtArt 51 -942.8977 1987.795 2170.745
## mtArt+I 52 -934.8133 1973.627 2160.164
## mtArt+G(4) 52 -934.9639 1973.928 2160.465
## mtArt+G(4)+I 53 -934.8252 1975.65 2165.775
## MtZoa 51 -937.3073 1976.615 2159.564
## MtZoa+I 52 -929.3564 1962.713 2149.25
## MtZoa+G(4) 52 -929.4937 1962.987 2149.524
## MtZoa+G(4)+I 53 -929.3668 1964.734 2154.858
## mtREV24 51 -949.6037 2001.207 2184.157
## mtREV24+I 52 -939.9664 1983.933 2170.47
## mtREV24+G(4) 52 -940.273 1984.546 2171.083
## mtREV24+G(4)+I 53 -939.9751 1985.95 2176.074
## VT 51 -978.9772 2059.954 2242.904
## VT+I 52 -969.715 2043.43 2229.967
## VT+G(4) 52 -970.0259 2044.052 2230.589
## VT+G(4)+I 53 -969.7784 2045.557 2235.681
## RtREV 51 -991.7055 2085.411 2268.361
## RtREV+I 52 -980.9445 2065.889 2252.426
## RtREV+G(4) 52 -981.5218 2067.044 2253.581
## RtREV+G(4)+I 53 -980.9558 2067.912 2258.036
## HIVw 51 -1024.179 2150.359 2333.308
## HIVw+I 52 -1008.35 2120.701 2307.238
## HIVw+G(4) 52 -1010.246 2124.493 2311.03
## HIVw+G(4)+I 53 -1008.504 2123.008 2313.133
## HIVb 51 -1001.539 2105.079 2288.028
## HIVb+I 52 -987.7643 2079.529 2266.065
## HIVb+G(4) 52 -989.0728 2082.146 2268.683
## HIVb+G(4)+I 53 -987.817 2081.634 2271.758
## FLU 51 -996.7898 2095.58 2278.529
## FLU+I 52 -985.172 2074.344 2260.881
## FLU+G(4) 52 -985.963 2075.926 2262.463
## FLU+G(4)+I 53 -985.282 2076.564 2266.688
## Blosum62 51 -984.9206 2071.841 2254.791
## Blosum62+I 52 -975.0209 2054.042 2240.579
## Blosum62+G(4) 52 -975.5213 2055.043 2241.58
## Blosum62+G(4)+I 53 -975.0382 2056.076 2246.201
## Dayhoff_DCMut 51 -1001.001 2104.001 2286.951
## Dayhoff_DCMut+I 52 -989.4565 2082.913 2269.45
## Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 2271.406
## Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 2275.42
## JTT_DCMut 51 -985.6565 2073.313 2256.263
## JTT_DCMut+I 52 -974.5499 2053.1 2239.637
## JTT_DCMut+G(4) 52 -975.4365 2054.873 2241.41
## JTT_DCMut+G(4)+I 53 -974.6698 2055.34 2245.464Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_4_modeltest, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"mySequences_align_aa_gr_ext_4_modeltest[order(mySequences_align_aa_gr_ext_4_modeltest$AIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -929.3564 1962.713 4.448504e-01 1988.470
## 31 MtZoa+G(4) 52 -929.4937 1962.987 3.877679e-01 1988.744
## 32 MtZoa+G(4)+I 53 -929.3668 1964.734 1.619574e-01 1991.607
## 26 mtArt+I 52 -934.8133 1973.627 1.898024e-03 1999.384
## 27 mtArt+G(4) 52 -934.9639 1973.928 1.632722e-03 1999.685
## 28 mtArt+G(4)+I 53 -934.8252 1975.650 6.899977e-04 2002.524
## 29 MtZoa 51 -937.3073 1976.615 4.260545e-04 2001.284
## 22 mtmam+I 52 -936.5416 1977.083 3.370915e-04 2002.840
## 23 mtmam+G(4) 52 -936.6824 1977.365 2.928163e-04 2003.122
## 24 mtmam+G(4)+I 53 -936.5512 1979.102 1.228157e-04 2005.976
## 34 mtREV24+I 52 -939.9664 1983.933 1.097381e-05 2009.690
## 35 mtREV24+G(4) 52 -940.2730 1984.546 8.076048e-06 2010.303
## 36 mtREV24+G(4)+I 53 -939.9751 1985.950 4.002159e-06 2012.823
## 25 mtArt 51 -942.8977 1987.795 1.590768e-06 2012.465
## 21 mtmam 51 -945.8698 1993.740 8.144187e-08 2018.409
## 33 mtREV24 51 -949.6037 2001.207 1.946282e-09 2025.877
## 18 cpREV+I 52 -963.9911 2031.982 4.041605e-16 2057.739
## 19 cpREV+G(4) 52 -964.8180 2033.636 1.767838e-16 2059.393
## 20 cpREV+G(4)+I 53 -964.1154 2034.231 1.313106e-16 2061.104
## 38 VT+I 52 -969.7150 2043.430 1.320329e-18 2069.187
## 39 VT+G(4) 52 -970.0259 2044.052 9.675497e-19 2069.809
## 40 VT+G(4)+I 53 -969.7784 2045.557 4.559211e-19 2072.430
## 6 JTT+I 52 -973.9716 2051.943 1.870978e-20 2077.700
## 17 cpREV 51 -975.0217 2052.043 1.779666e-20 2076.713
## 66 JTT_DCMut+I 52 -974.5499 2053.100 1.049348e-20 2078.857
## 7 JTT+G(4) 52 -974.8447 2053.689 7.814648e-21 2079.446
## 58 Blosum62+I 52 -975.0209 2054.042 6.552254e-21 2079.799
## 8 JTT+G(4)+I 53 -974.0697 2054.139 6.240306e-21 2081.013
## 67 JTT_DCMut+G(4) 52 -975.4365 2054.873 4.323898e-21 2080.630
## 59 Blosum62+G(4) 52 -975.5213 2055.043 3.972329e-21 2080.800
## 68 JTT_DCMut+G(4)+I 53 -974.6698 2055.340 3.424422e-21 2082.213
## 60 Blosum62+G(4)+I 53 -975.0382 2056.076 2.369018e-21 2082.950
## 10 LG+I 52 -976.3740 2056.748 1.693243e-21 2082.505
## 11 LG+G(4) 52 -977.0353 2058.071 8.740773e-22 2083.828
## 12 LG+G(4)+I 53 -976.3983 2058.797 6.079550e-22 2085.670
## 37 VT 51 -978.9772 2059.954 3.407855e-22 2084.624
## 2 WAG+I 52 -978.0493 2060.099 3.170706e-22 2085.856
## 3 WAG+G(4) 52 -979.0440 2062.088 1.172617e-22 2087.845
## 4 WAG+G(4)+I 53 -978.0852 2062.170 1.125342e-22 2089.044
## 42 RtREV+I 52 -980.9445 2065.889 1.753017e-23 2091.646
## 43 RtREV+G(4) 52 -981.5218 2067.044 9.841342e-24 2092.801
## 44 RtREV+G(4)+I 53 -980.9558 2067.912 6.376483e-24 2094.785
## 57 Blosum62 51 -984.9206 2071.841 8.938842e-25 2096.511
## 5 JTT 51 -985.0266 2072.053 8.040085e-25 2096.723
## 65 JTT_DCMut 51 -985.6565 2073.313 4.282641e-25 2097.983
## 54 FLU+I 52 -985.1720 2074.344 2.557514e-25 2100.101
## 9 LG 51 -986.8872 2075.774 1.250836e-25 2100.444
## 55 FLU+G(4) 52 -985.9630 2075.926 1.159587e-25 2101.683
## 56 FLU+G(4)+I 53 -985.2820 2076.564 8.428459e-26 2103.437
## 50 HIVb+I 52 -987.7643 2079.529 1.914256e-26 2105.286
## 1 WAG 51 -989.4844 2080.969 9.316362e-27 2105.639
## 52 HIVb+G(4)+I 53 -987.8170 2081.634 6.680825e-27 2108.507
## 51 HIVb+G(4) 52 -989.0728 2082.146 5.172561e-27 2107.903
## 14 Dayhoff+I 52 -989.3875 2082.775 3.776241e-27 2108.532
## 62 Dayhoff_DCMut+I 52 -989.4565 2082.913 3.524502e-27 2108.670
## 15 Dayhoff+G(4) 52 -990.3689 2084.738 1.415238e-27 2110.495
## 63 Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 1.325145e-27 2110.626
## 16 Dayhoff+G(4)+I 53 -989.5790 2085.158 1.147093e-27 2112.031
## 64 Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 1.070455e-27 2112.169
## 41 RtREV 51 -991.7055 2085.411 1.010702e-27 2110.081
## 53 FLU 51 -996.7898 2095.580 6.259500e-30 2120.249
## 13 Dayhoff 51 -1000.9445 2103.889 9.821701e-32 2128.559
## 61 Dayhoff_DCMut 51 -1001.0005 2104.001 9.286583e-32 2128.671
## 49 HIVb 51 -1001.5393 2105.079 5.418406e-32 2129.748
## 46 HIVw+I 52 -1008.3504 2120.701 2.195655e-35 2146.458
## 48 HIVw+G(4)+I 53 -1008.5042 2123.008 6.925546e-36 2149.882
## 47 HIVw+G(4) 52 -1010.2463 2124.493 3.297493e-36 2150.250
## 45 HIVw 51 -1024.1793 2150.359 7.970257e-42 2175.028
## AICcw BIC
## 30 4.779801e-01 2149.250
## 31 4.166464e-01 2149.524
## 32 9.958875e-02 2154.858
## 26 2.039377e-03 2160.164
## 27 1.754317e-03 2160.465
## 28 4.242845e-04 2165.775
## 29 7.884106e-04 2159.564
## 22 3.621959e-04 2163.620
## 23 3.146234e-04 2163.902
## 24 7.552026e-05 2169.227
## 34 1.179107e-05 2170.470
## 35 8.677501e-06 2171.083
## 36 2.460956e-06 2176.074
## 25 2.943704e-06 2170.745
## 21 1.507076e-07 2176.689
## 33 3.601581e-09 2184.157
## 18 4.342598e-16 2218.519
## 19 1.899495e-16 2220.173
## 20 8.074384e-17 2224.355
## 38 1.418659e-18 2229.967
## 39 1.039607e-18 2230.589
## 40 2.803491e-19 2235.681
## 6 2.010316e-20 2238.480
## 17 3.293259e-20 2234.993
## 66 1.127497e-20 2239.637
## 7 8.396633e-21 2240.226
## 58 7.040224e-21 2240.579
## 8 3.837208e-21 2244.263
## 67 4.645915e-21 2241.410
## 59 4.268163e-21 2241.580
## 68 2.105701e-21 2245.464
## 60 1.456726e-21 2246.201
## 10 1.819345e-21 2243.285
## 11 9.391731e-22 2244.607
## 12 3.738358e-22 2248.921
## 37 6.306210e-22 2242.904
## 2 3.406840e-22 2246.636
## 3 1.259946e-22 2248.625
## 4 6.919809e-23 2252.295
## 42 1.883571e-23 2252.426
## 43 1.057426e-23 2253.581
## 44 3.920945e-24 2258.036
## 57 1.654126e-24 2254.791
## 5 1.487812e-24 2255.003
## 65 7.924995e-25 2256.263
## 54 2.747981e-25 2260.881
## 9 2.314662e-25 2258.724
## 55 1.245946e-25 2262.463
## 56 5.182719e-26 2266.688
## 50 2.056818e-26 2266.065
## 1 1.723986e-26 2263.919
## 52 4.108087e-27 2271.758
## 51 5.557781e-27 2268.683
## 14 4.057471e-27 2269.312
## 62 3.786984e-27 2269.450
## 15 1.520636e-27 2271.275
## 63 1.423833e-27 2271.406
## 16 7.053559e-28 2275.282
## 64 6.582307e-28 2275.420
## 41 1.870297e-27 2268.361
## 53 1.158316e-29 2278.529
## 13 1.817498e-31 2286.839
## 61 1.718475e-31 2286.951
## 49 1.002672e-31 2288.028
## 46 2.359173e-35 2307.238
## 48 4.258567e-36 2313.133
## 47 3.543069e-36 2311.030
## 45 1.474890e-41 2333.308mySequences_align_aa_gr_ext_4_modeltest[order(mySequences_align_aa_gr_ext_4_modeltest$BIC), ]## Model df logLik AIC AICw AICc
## 30 MtZoa+I 52 -929.3564 1962.713 4.448504e-01 1988.470
## 31 MtZoa+G(4) 52 -929.4937 1962.987 3.877679e-01 1988.744
## 32 MtZoa+G(4)+I 53 -929.3668 1964.734 1.619574e-01 1991.607
## 29 MtZoa 51 -937.3073 1976.615 4.260545e-04 2001.284
## 26 mtArt+I 52 -934.8133 1973.627 1.898024e-03 1999.384
## 27 mtArt+G(4) 52 -934.9639 1973.928 1.632722e-03 1999.685
## 22 mtmam+I 52 -936.5416 1977.083 3.370915e-04 2002.840
## 23 mtmam+G(4) 52 -936.6824 1977.365 2.928163e-04 2003.122
## 28 mtArt+G(4)+I 53 -934.8252 1975.650 6.899977e-04 2002.524
## 24 mtmam+G(4)+I 53 -936.5512 1979.102 1.228157e-04 2005.976
## 34 mtREV24+I 52 -939.9664 1983.933 1.097381e-05 2009.690
## 25 mtArt 51 -942.8977 1987.795 1.590768e-06 2012.465
## 35 mtREV24+G(4) 52 -940.2730 1984.546 8.076048e-06 2010.303
## 36 mtREV24+G(4)+I 53 -939.9751 1985.950 4.002159e-06 2012.823
## 21 mtmam 51 -945.8698 1993.740 8.144187e-08 2018.409
## 33 mtREV24 51 -949.6037 2001.207 1.946282e-09 2025.877
## 18 cpREV+I 52 -963.9911 2031.982 4.041605e-16 2057.739
## 19 cpREV+G(4) 52 -964.8180 2033.636 1.767838e-16 2059.393
## 20 cpREV+G(4)+I 53 -964.1154 2034.231 1.313106e-16 2061.104
## 38 VT+I 52 -969.7150 2043.430 1.320329e-18 2069.187
## 39 VT+G(4) 52 -970.0259 2044.052 9.675497e-19 2069.809
## 17 cpREV 51 -975.0217 2052.043 1.779666e-20 2076.713
## 40 VT+G(4)+I 53 -969.7784 2045.557 4.559211e-19 2072.430
## 6 JTT+I 52 -973.9716 2051.943 1.870978e-20 2077.700
## 66 JTT_DCMut+I 52 -974.5499 2053.100 1.049348e-20 2078.857
## 7 JTT+G(4) 52 -974.8447 2053.689 7.814648e-21 2079.446
## 58 Blosum62+I 52 -975.0209 2054.042 6.552254e-21 2079.799
## 67 JTT_DCMut+G(4) 52 -975.4365 2054.873 4.323898e-21 2080.630
## 59 Blosum62+G(4) 52 -975.5213 2055.043 3.972329e-21 2080.800
## 37 VT 51 -978.9772 2059.954 3.407855e-22 2084.624
## 10 LG+I 52 -976.3740 2056.748 1.693243e-21 2082.505
## 8 JTT+G(4)+I 53 -974.0697 2054.139 6.240306e-21 2081.013
## 11 LG+G(4) 52 -977.0353 2058.071 8.740773e-22 2083.828
## 68 JTT_DCMut+G(4)+I 53 -974.6698 2055.340 3.424422e-21 2082.213
## 60 Blosum62+G(4)+I 53 -975.0382 2056.076 2.369018e-21 2082.950
## 2 WAG+I 52 -978.0493 2060.099 3.170706e-22 2085.856
## 3 WAG+G(4) 52 -979.0440 2062.088 1.172617e-22 2087.845
## 12 LG+G(4)+I 53 -976.3983 2058.797 6.079550e-22 2085.670
## 4 WAG+G(4)+I 53 -978.0852 2062.170 1.125342e-22 2089.044
## 42 RtREV+I 52 -980.9445 2065.889 1.753017e-23 2091.646
## 43 RtREV+G(4) 52 -981.5218 2067.044 9.841342e-24 2092.801
## 57 Blosum62 51 -984.9206 2071.841 8.938842e-25 2096.511
## 5 JTT 51 -985.0266 2072.053 8.040085e-25 2096.723
## 65 JTT_DCMut 51 -985.6565 2073.313 4.282641e-25 2097.983
## 44 RtREV+G(4)+I 53 -980.9558 2067.912 6.376483e-24 2094.785
## 9 LG 51 -986.8872 2075.774 1.250836e-25 2100.444
## 54 FLU+I 52 -985.1720 2074.344 2.557514e-25 2100.101
## 55 FLU+G(4) 52 -985.9630 2075.926 1.159587e-25 2101.683
## 1 WAG 51 -989.4844 2080.969 9.316362e-27 2105.639
## 50 HIVb+I 52 -987.7643 2079.529 1.914256e-26 2105.286
## 56 FLU+G(4)+I 53 -985.2820 2076.564 8.428459e-26 2103.437
## 41 RtREV 51 -991.7055 2085.411 1.010702e-27 2110.081
## 51 HIVb+G(4) 52 -989.0728 2082.146 5.172561e-27 2107.903
## 14 Dayhoff+I 52 -989.3875 2082.775 3.776241e-27 2108.532
## 62 Dayhoff_DCMut+I 52 -989.4565 2082.913 3.524502e-27 2108.670
## 15 Dayhoff+G(4) 52 -990.3689 2084.738 1.415238e-27 2110.495
## 63 Dayhoff_DCMut+G(4) 52 -990.4347 2084.869 1.325145e-27 2110.626
## 52 HIVb+G(4)+I 53 -987.8170 2081.634 6.680825e-27 2108.507
## 16 Dayhoff+G(4)+I 53 -989.5790 2085.158 1.147093e-27 2112.031
## 64 Dayhoff_DCMut+G(4)+I 53 -989.6481 2085.296 1.070455e-27 2112.169
## 53 FLU 51 -996.7898 2095.580 6.259500e-30 2120.249
## 13 Dayhoff 51 -1000.9445 2103.889 9.821701e-32 2128.559
## 61 Dayhoff_DCMut 51 -1001.0005 2104.001 9.286583e-32 2128.671
## 49 HIVb 51 -1001.5393 2105.079 5.418406e-32 2129.748
## 46 HIVw+I 52 -1008.3504 2120.701 2.195655e-35 2146.458
## 47 HIVw+G(4) 52 -1010.2463 2124.493 3.297493e-36 2150.250
## 48 HIVw+G(4)+I 53 -1008.5042 2123.008 6.925546e-36 2149.882
## 45 HIVw 51 -1024.1793 2150.359 7.970257e-42 2175.028
## AICcw BIC
## 30 4.779801e-01 2149.250
## 31 4.166464e-01 2149.524
## 32 9.958875e-02 2154.858
## 29 7.884106e-04 2159.564
## 26 2.039377e-03 2160.164
## 27 1.754317e-03 2160.465
## 22 3.621959e-04 2163.620
## 23 3.146234e-04 2163.902
## 28 4.242845e-04 2165.775
## 24 7.552026e-05 2169.227
## 34 1.179107e-05 2170.470
## 25 2.943704e-06 2170.745
## 35 8.677501e-06 2171.083
## 36 2.460956e-06 2176.074
## 21 1.507076e-07 2176.689
## 33 3.601581e-09 2184.157
## 18 4.342598e-16 2218.519
## 19 1.899495e-16 2220.173
## 20 8.074384e-17 2224.355
## 38 1.418659e-18 2229.967
## 39 1.039607e-18 2230.589
## 17 3.293259e-20 2234.993
## 40 2.803491e-19 2235.681
## 6 2.010316e-20 2238.480
## 66 1.127497e-20 2239.637
## 7 8.396633e-21 2240.226
## 58 7.040224e-21 2240.579
## 67 4.645915e-21 2241.410
## 59 4.268163e-21 2241.580
## 37 6.306210e-22 2242.904
## 10 1.819345e-21 2243.285
## 8 3.837208e-21 2244.263
## 11 9.391731e-22 2244.607
## 68 2.105701e-21 2245.464
## 60 1.456726e-21 2246.201
## 2 3.406840e-22 2246.636
## 3 1.259946e-22 2248.625
## 12 3.738358e-22 2248.921
## 4 6.919809e-23 2252.295
## 42 1.883571e-23 2252.426
## 43 1.057426e-23 2253.581
## 57 1.654126e-24 2254.791
## 5 1.487812e-24 2255.003
## 65 7.924995e-25 2256.263
## 44 3.920945e-24 2258.036
## 9 2.314662e-25 2258.724
## 54 2.747981e-25 2260.881
## 55 1.245946e-25 2262.463
## 1 1.723986e-26 2263.919
## 50 2.056818e-26 2266.065
## 56 5.182719e-26 2266.688
## 41 1.870297e-27 2268.361
## 51 5.557781e-27 2268.683
## 14 4.057471e-27 2269.312
## 62 3.786984e-27 2269.450
## 15 1.520636e-27 2271.275
## 63 1.423833e-27 2271.406
## 52 4.108087e-27 2271.758
## 16 7.053559e-28 2275.282
## 64 6.582307e-28 2275.420
## 53 1.158316e-29 2278.529
## 13 1.817498e-31 2286.839
## 61 1.718475e-31 2286.951
## 49 1.002672e-31 2288.028
## 46 2.359173e-35 2307.238
## 47 3.543069e-36 2311.030
## 48 4.258567e-36 2313.133
## 45 1.474890e-41 2333.308Meilleur modele : MtZoa+I
env$`MtZoa+I`## pml(tree = `tree_MtZoa+I`, data = data, model = "MtZoa", inv = 0.750243950421922)Construction arbres
# Matrice de ditance
dm_aa_gr_ext_4 <- dist.ml(mySequences_align_aa_gr_ext_4_phangorn, model = "MtZoa")
# Construction arbre NJ
treeNJ_aa_gr_ext_4 <- NJ(dm_aa_gr_ext_4)Integration des parametres
fit_aa_gr_ext_4 = pml(treeNJ_aa_gr_ext_4, data=mySequences_align_aa_gr_ext_4_phangorn)
fitMtZoa_aa_gr_ext_4 <- update(fit_aa_gr_ext_4, model="MtZoa", inv=0.7535778946048)
fitMtZoa_aa_gr_ext_4 <- optim.pml(fitMtZoa_aa_gr_ext_4, model="MtZoa", optInv=TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_aa_gr_ext_4 = bootstrap.pml(fitMtZoa_aa_gr_ext_4, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitMtZoa_aa_gr_ext_4$tree), bs_aa_gr_ext_4, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
Les quatres ensembles
Fusionner avec les cetaces
Sequences_groupe_externe_5 <- c(myNewSequences, myExterneSequences)ADN
Alignement
mySequences_align_gr_ext_5 = AlignSeqs(Sequences_groupe_externe_5, gapOpening = c(-18,-16), gapExtension = c(-2,-1)) ## Determining distance matrix based on shared 11-mers:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 0.7 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.61 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secsRecherche du meilleur modele
mySequences_align_gr_ext_5_ape = as.DNAbin(mySequences_align_gr_ext_5)
mySequences_align_gr_ext_5_phangorn = as.phyDat(mySequences_align_gr_ext_5_ape)
mySequences_gr_ext_5_modelTest = phangorn::modelTest(mySequences_align_gr_ext_5_phangorn)## Model df logLik AIC BIC
## JC 63 -32775.4 65676.79 66162.25
## JC+I 64 -32237.33 64602.66 65095.83
## JC+G(4) 64 -32237.07 64602.14 65095.31
## JC+G(4)+I 65 -32223.44 64576.88 65077.75
## F81 66 -32078.43 64288.86 64797.44
## F81+I 67 -31508.49 63150.97 63667.25
## F81+G(4) 67 -31502.67 63139.33 63655.61
## F81+G(4)+I 68 -31491.05 63118.1 63642.09
## K80 64 -31738.74 63605.47 64098.64
## K80+I 65 -31131.18 62392.35 62893.22
## K80+G(4) 65 -31079.78 62289.57 62790.43
## K80+G(4)+I 66 -31074.41 62280.82 62789.39
## HKY 67 -31004.41 62142.81 62659.09
## HKY+I 68 -30302.17 60740.35 61264.33
## HKY+G(4) 68 -30240.26 60616.52 61140.5
## HKY+G(4)+I 69 -30233.94 60605.89 61137.58
## TrNe 65 -31696.4 63522.8 64023.66
## TrNe+I 66 -31089.78 62311.56 62820.14
## TrNe+G(4) 66 -31056.75 62245.5 62754.07
## TrNe+G(4)+I 67 -31042.66 62219.32 62735.6
## TrN 68 -30999.16 62134.31 62658.29
## TrN+I 69 -30301.63 60741.27 61272.96
## TrN+G(4) 69 -30240.22 60618.45 61150.14
## TrN+G(4)+I 70 -30233.7 60607.41 61146.8
## TPM1 65 -31738.74 63607.47 64108.34
## TPM1+I 66 -31131.17 62394.34 62902.91
## TPM1+G(4) 66 -31079.74 62291.47 62800.04
## TPM1+G(4)+I 67 -31074.38 62282.76 62799.04
## K81 65 -31738.74 63607.47 64108.34
## K81+I 66 -31131.17 62394.34 62902.91
## K81+G(4) 66 -31079.74 62291.47 62800.04
## K81+G(4)+I 67 -31074.38 62282.76 62799.04
## TPM1u 68 -31004.4 62144.8 62668.78
## TPM1u+I 69 -30302.04 60742.08 61273.77
## TPM1u+G(4) 69 -30240.09 60618.17 61149.86
## TPM1u+G(4)+I 70 -30233.72 60607.43 61146.83
## TPM2 65 -31674.86 63479.71 63980.58
## TPM2+I 66 -31098.51 62329.02 62837.6
## TPM2+G(4) 66 -31060.17 62252.33 62760.9
## TPM2+G(4)+I 67 -31051.86 62237.71 62753.99
## TPM2u 68 -30973.91 62083.82 62607.8
## TPM2u+I 69 -30295.92 60729.84 61261.53
## TPM2u+G(4) 69 -30238.74 60615.48 61147.17
## TPM2u+G(4)+I 70 -30231.98 60603.96 61143.36
## TPM3 65 -31737.58 63605.17 64106.03
## TPM3+I 66 -31126.63 62385.25 62893.82
## TPM3+G(4) 66 -31077.06 62286.12 62794.69
## TPM3+G(4)+I 67 -31071.43 62276.86 62793.14
## TPM3u 68 -31002.89 62141.77 62665.76
## TPM3u+I 69 -30298.72 60735.45 61267.14
## TPM3u+G(4) 69 -30238.04 60614.08 61145.77
## TPM3u+G(4)+I 70 -30231.37 60602.74 61142.14
## TIM1e 66 -31696.4 63524.8 64033.37
## TIM1e+I 67 -31089.78 62313.55 62829.83
## TIM1e+G(4) 67 -31056.73 62247.46 62763.74
## TIM1e+G(4)+I 68 -31042.65 62221.3 62745.28
## TIM1 69 -30999.15 62136.3 62667.99
## TIM1+I 70 -30301.51 60743.02 61282.41
## TIM1+G(4) 70 -30240.05 60620.1 61159.49
## TIM1+G(4)+I 71 -30233.48 60608.97 61156.07
## TIM2e 66 -31632.21 63396.43 63905
## TIM2e+I 67 -31051.59 62237.18 62753.45
## TIM2e+G(4) 67 -31032.95 62199.91 62716.18
## TIM2e+G(4)+I 68 -31015.47 62166.95 62690.93
## TIM2 69 -30968.65 62075.3 62606.99
## TIM2+I 70 -30294.96 60729.92 61269.32
## TIM2+G(4) 70 -30238.73 60617.46 61156.86
## TIM2+G(4)+I 71 -30231.62 60605.25 61152.35
## TIM3e 66 -31695.21 63522.42 64030.99
## TIM3e+I 67 -31085.09 62304.19 62820.47
## TIM3e+G(4) 67 -31054.27 62242.54 62758.82
## TIM3e+G(4)+I 68 -31039.84 62215.68 62739.66
## TIM3 69 -30997.62 62133.24 62664.93
## TIM3+I 70 -30298.17 60736.35 61275.74
## TIM3+G(4) 70 -30237.99 60615.99 61155.38
## TIM3+G(4)+I 71 -30231.15 60604.29 61151.39
## TVMe 67 -31673.13 63480.26 63996.54
## TVMe+I 68 -31093.79 62323.58 62847.57
## TVMe+G(4) 68 -31057.02 62250.04 62774.03
## TVMe+G(4)+I 69 -31048.64 62235.27 62766.96
## TVM 70 -30971.65 62083.3 62622.69
## TVM+I 71 -30291.76 60725.53 61272.63
## TVM+G(4) 71 -30236.27 60614.54 61161.64
## TVM+G(4)+I 72 -30229.22 60602.44 61157.25
## SYM 68 -31630.42 63396.84 63920.83
## SYM+I 69 -31046.8 62231.61 62763.3
## SYM+G(4) 69 -31030.03 62198.05 62729.74
## SYM+G(4)+I 70 -31012.39 62164.78 62704.18
## GTR 71 -30966.37 62074.74 62621.84
## GTR+I 72 -30290.79 60725.59 61280.4
## GTR+G(4) 72 -30236.26 60616.51 61171.32
## GTR+G(4)+I 73 -30228.88 60603.76 61166.27Trouver le meilleur modele
env <- attr(mySequences_gr_ext_5_modelTest, "env")
ls(env=env)## [1] "data" "F81" "F81+G(4)"
## [4] "F81+G(4)+I" "F81+I" "GTR"
## [7] "GTR+G(4)" "GTR+G(4)+I" "GTR+I"
## [10] "HKY" "HKY+G(4)" "HKY+G(4)+I"
## [13] "HKY+I" "JC" "JC+G(4)"
## [16] "JC+G(4)+I" "JC+I" "K80"
## [19] "K80+G(4)" "K80+G(4)+I" "K80+I"
## [22] "K81" "K81+G(4)" "K81+G(4)+I"
## [25] "K81+I" "SYM" "SYM+G(4)"
## [28] "SYM+G(4)+I" "SYM+I" "TIM1"
## [31] "TIM1+G(4)" "TIM1+G(4)+I" "TIM1+I"
## [34] "TIM1e" "TIM1e+G(4)" "TIM1e+G(4)+I"
## [37] "TIM1e+I" "TIM2" "TIM2+G(4)"
## [40] "TIM2+G(4)+I" "TIM2+I" "TIM2e"
## [43] "TIM2e+G(4)" "TIM2e+G(4)+I" "TIM2e+I"
## [46] "TIM3" "TIM3+G(4)" "TIM3+G(4)+I"
## [49] "TIM3+I" "TIM3e" "TIM3e+G(4)"
## [52] "TIM3e+G(4)+I" "TIM3e+I" "TPM1"
## [55] "TPM1+G(4)" "TPM1+G(4)+I" "TPM1+I"
## [58] "TPM1u" "TPM1u+G(4)" "TPM1u+G(4)+I"
## [61] "TPM1u+I" "TPM2" "TPM2+G(4)"
## [64] "TPM2+G(4)+I" "TPM2+I" "TPM2u"
## [67] "TPM2u+G(4)" "TPM2u+G(4)+I" "TPM2u+I"
## [70] "TPM3" "TPM3+G(4)" "TPM3+G(4)+I"
## [73] "TPM3+I" "TPM3u" "TPM3u+G(4)"
## [76] "TPM3u+G(4)+I" "TPM3u+I" "tree_F81"
## [79] "tree_F81+G(4)" "tree_F81+G(4)+I" "tree_F81+I"
## [82] "tree_GTR" "tree_GTR+G(4)" "tree_GTR+G(4)+I"
## [85] "tree_GTR+I" "tree_HKY" "tree_HKY+G(4)"
## [88] "tree_HKY+G(4)+I" "tree_HKY+I" "tree_JC"
## [91] "tree_JC+G(4)" "tree_JC+G(4)+I" "tree_JC+I"
## [94] "tree_K80" "tree_K80+G(4)" "tree_K80+G(4)+I"
## [97] "tree_K80+I" "tree_K81" "tree_K81+G(4)"
## [100] "tree_K81+G(4)+I" "tree_K81+I" "tree_SYM"
## [103] "tree_SYM+G(4)" "tree_SYM+G(4)+I" "tree_SYM+I"
## [106] "tree_TIM1" "tree_TIM1+G(4)" "tree_TIM1+G(4)+I"
## [109] "tree_TIM1+I" "tree_TIM1e" "tree_TIM1e+G(4)"
## [112] "tree_TIM1e+G(4)+I" "tree_TIM1e+I" "tree_TIM2"
## [115] "tree_TIM2+G(4)" "tree_TIM2+G(4)+I" "tree_TIM2+I"
## [118] "tree_TIM2e" "tree_TIM2e+G(4)" "tree_TIM2e+G(4)+I"
## [121] "tree_TIM2e+I" "tree_TIM3" "tree_TIM3+G(4)"
## [124] "tree_TIM3+G(4)+I" "tree_TIM3+I" "tree_TIM3e"
## [127] "tree_TIM3e+G(4)" "tree_TIM3e+G(4)+I" "tree_TIM3e+I"
## [130] "tree_TPM1" "tree_TPM1+G(4)" "tree_TPM1+G(4)+I"
## [133] "tree_TPM1+I" "tree_TPM1u" "tree_TPM1u+G(4)"
## [136] "tree_TPM1u+G(4)+I" "tree_TPM1u+I" "tree_TPM2"
## [139] "tree_TPM2+G(4)" "tree_TPM2+G(4)+I" "tree_TPM2+I"
## [142] "tree_TPM2u" "tree_TPM2u+G(4)" "tree_TPM2u+G(4)+I"
## [145] "tree_TPM2u+I" "tree_TPM3" "tree_TPM3+G(4)"
## [148] "tree_TPM3+G(4)+I" "tree_TPM3+I" "tree_TPM3u"
## [151] "tree_TPM3u+G(4)" "tree_TPM3u+G(4)+I" "tree_TPM3u+I"
## [154] "tree_TrN" "tree_TrN+G(4)" "tree_TrN+G(4)+I"
## [157] "tree_TrN+I" "tree_TrNe" "tree_TrNe+G(4)"
## [160] "tree_TrNe+G(4)+I" "tree_TrNe+I" "tree_TVM"
## [163] "tree_TVM+G(4)" "tree_TVM+G(4)+I" "tree_TVM+I"
## [166] "tree_TVMe" "tree_TVMe+G(4)" "tree_TVMe+G(4)+I"
## [169] "tree_TVMe+I" "TrN" "TrN+G(4)"
## [172] "TrN+G(4)+I" "TrN+I" "TrNe"
## [175] "TrNe+G(4)" "TrNe+G(4)+I" "TrNe+I"
## [178] "TVM" "TVM+G(4)" "TVM+G(4)+I"
## [181] "TVM+I" "TVMe" "TVMe+G(4)"
## [184] "TVMe+G(4)+I" "TVMe+I"mySequences_gr_ext_5_modelTest[order(mySequences_gr_ext_5_modelTest$AIC), ]## Model df logLik AIC AICw AICc AICcw
## 84 TVM+G(4)+I 72 -30229.22 60602.44 2.576621e-01 60603.09 2.555028e-01
## 52 TPM3u+G(4)+I 70 -30231.37 60602.74 2.215058e-01 60603.35 2.235370e-01
## 92 GTR+G(4)+I 73 -30228.88 60603.76 1.333119e-01 60604.42 1.310159e-01
## 44 TPM2u+G(4)+I 70 -30231.98 60603.96 1.204924e-01 60604.57 1.215973e-01
## 76 TIM3+G(4)+I 71 -30231.15 60604.29 1.022371e-01 60604.92 1.022798e-01
## 68 TIM2+G(4)+I 71 -30231.62 60605.25 6.335246e-02 60605.87 6.337894e-02
## 16 HKY+G(4)+I 69 -30233.94 60605.89 4.597245e-02 60606.48 4.679408e-02
## 24 TrN+G(4)+I 70 -30233.70 60607.41 2.150824e-02 60608.02 2.170547e-02
## 36 TPM1u+G(4)+I 70 -30233.72 60607.43 2.122298e-02 60608.04 2.141759e-02
## 60 TIM1+G(4)+I 71 -30233.48 60608.97 9.867728e-03 60609.59 9.871852e-03
## 51 TPM3u+G(4) 69 -30238.04 60614.08 7.665745e-04 60614.67 7.802749e-04
## 83 TVM+G(4) 71 -30236.27 60614.54 6.094845e-04 60615.16 6.097392e-04
## 43 TPM2u+G(4) 69 -30238.74 60615.48 3.793342e-04 60616.07 3.861137e-04
## 75 TIM3+G(4) 70 -30237.99 60615.99 2.946165e-04 60616.60 2.973180e-04
## 91 GTR+G(4) 72 -30236.26 60616.51 2.268411e-04 60617.16 2.249401e-04
## 15 HKY+G(4) 68 -30240.26 60616.52 2.262507e-04 60617.09 2.322516e-04
## 67 TIM2+G(4) 70 -30238.73 60617.46 1.408620e-04 60618.07 1.421537e-04
## 35 TPM1u+G(4) 69 -30240.09 60618.17 9.879058e-05 60618.77 1.005562e-04
## 23 TrN+G(4) 69 -30240.22 60618.45 8.625433e-05 60619.04 8.779589e-05
## 59 TIM1+G(4) 70 -30240.05 60620.10 3.778567e-05 60620.70 3.813215e-05
## 82 TVM+I 71 -30291.76 60725.53 4.827230e-28 60726.15 4.829248e-28
## 90 GTR+I 72 -30290.79 60725.59 4.676748e-28 60726.23 4.637556e-28
## 42 TPM2u+I 69 -30295.92 60729.84 5.576489e-29 60730.43 5.676154e-29
## 66 TIM2+I 70 -30294.96 60729.92 5.356339e-29 60730.53 5.405454e-29
## 50 TPM3u+I 69 -30298.72 60735.45 3.377990e-30 60736.04 3.438362e-30
## 74 TIM3+I 70 -30298.17 60736.35 2.156340e-30 60736.96 2.176113e-30
## 14 HKY+I 68 -30302.17 60740.35 2.918886e-31 60740.92 2.996305e-31
## 22 TrN+I 69 -30301.63 60741.27 1.842596e-31 60741.86 1.875528e-31
## 34 TPM1u+I 69 -30302.04 60742.08 1.225962e-31 60742.67 1.247873e-31
## 58 TIM1+I 70 -30301.51 60743.02 7.689664e-32 60743.62 7.760176e-32
## 89 GTR 71 -30966.37 62074.74 5.069114e-321 62075.37 5.074054e-321
## 65 TIM2 69 -30968.65 62075.30 3.833949e-321 62075.89 3.903119e-321
## 81 TVM 70 -30971.65 62083.30 6.916919e-323 62083.91 6.916919e-323
## 41 TPM2u 68 -30973.91 62083.82 5.434722e-323 62084.39 5.434722e-323
## 73 TIM3 69 -30997.62 62133.24 0.000000e+00 62133.83 0.000000e+00
## 21 TrN 68 -30999.16 62134.31 0.000000e+00 62134.88 0.000000e+00
## 57 TIM1 69 -30999.15 62136.30 0.000000e+00 62136.89 0.000000e+00
## 49 TPM3u 68 -31002.89 62141.77 0.000000e+00 62142.35 0.000000e+00
## 13 HKY 67 -31004.41 62142.81 0.000000e+00 62143.37 0.000000e+00
## 33 TPM1u 68 -31004.40 62144.80 0.000000e+00 62145.37 0.000000e+00
## 88 SYM+G(4)+I 70 -31012.39 62164.78 0.000000e+00 62165.39 0.000000e+00
## 64 TIM2e+G(4)+I 68 -31015.47 62166.95 0.000000e+00 62167.52 0.000000e+00
## 87 SYM+G(4) 69 -31030.03 62198.05 0.000000e+00 62198.64 0.000000e+00
## 63 TIM2e+G(4) 67 -31032.95 62199.91 0.000000e+00 62200.46 0.000000e+00
## 72 TIM3e+G(4)+I 68 -31039.84 62215.68 0.000000e+00 62216.25 0.000000e+00
## 20 TrNe+G(4)+I 67 -31042.66 62219.32 0.000000e+00 62219.88 0.000000e+00
## 56 TIM1e+G(4)+I 68 -31042.65 62221.30 0.000000e+00 62221.87 0.000000e+00
## 86 SYM+I 69 -31046.80 62231.61 0.000000e+00 62232.20 0.000000e+00
## 80 TVMe+G(4)+I 69 -31048.64 62235.27 0.000000e+00 62235.87 0.000000e+00
## 62 TIM2e+I 67 -31051.59 62237.18 0.000000e+00 62237.73 0.000000e+00
## 40 TPM2+G(4)+I 67 -31051.86 62237.71 0.000000e+00 62238.27 0.000000e+00
## 71 TIM3e+G(4) 67 -31054.27 62242.54 0.000000e+00 62243.10 0.000000e+00
## 19 TrNe+G(4) 66 -31056.75 62245.50 0.000000e+00 62246.04 0.000000e+00
## 55 TIM1e+G(4) 67 -31056.73 62247.46 0.000000e+00 62248.02 0.000000e+00
## 79 TVMe+G(4) 68 -31057.02 62250.04 0.000000e+00 62250.62 0.000000e+00
## 39 TPM2+G(4) 66 -31060.17 62252.33 0.000000e+00 62252.87 0.000000e+00
## 48 TPM3+G(4)+I 67 -31071.43 62276.86 0.000000e+00 62277.41 0.000000e+00
## 12 K80+G(4)+I 66 -31074.41 62280.82 0.000000e+00 62281.36 0.000000e+00
## 28 TPM1+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 32 K81+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 47 TPM3+G(4) 66 -31077.06 62286.12 0.000000e+00 62286.66 0.000000e+00
## 11 K80+G(4) 65 -31079.78 62289.57 0.000000e+00 62290.09 0.000000e+00
## 27 TPM1+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 31 K81+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 70 TIM3e+I 67 -31085.09 62304.19 0.000000e+00 62304.75 0.000000e+00
## 18 TrNe+I 66 -31089.78 62311.56 0.000000e+00 62312.10 0.000000e+00
## 54 TIM1e+I 67 -31089.78 62313.55 0.000000e+00 62314.11 0.000000e+00
## 78 TVMe+I 68 -31093.79 62323.58 0.000000e+00 62324.16 0.000000e+00
## 38 TPM2+I 66 -31098.51 62329.02 0.000000e+00 62329.57 0.000000e+00
## 46 TPM3+I 66 -31126.63 62385.25 0.000000e+00 62385.79 0.000000e+00
## 10 K80+I 65 -31131.18 62392.35 0.000000e+00 62392.88 0.000000e+00
## 26 TPM1+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 30 K81+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 8 F81+G(4)+I 68 -31491.05 63118.10 0.000000e+00 63118.68 0.000000e+00
## 7 F81+G(4) 67 -31502.67 63139.33 0.000000e+00 63139.89 0.000000e+00
## 6 F81+I 67 -31508.49 63150.97 0.000000e+00 63151.53 0.000000e+00
## 61 TIM2e 66 -31632.21 63396.43 0.000000e+00 63396.97 0.000000e+00
## 85 SYM 68 -31630.42 63396.84 0.000000e+00 63397.42 0.000000e+00
## 37 TPM2 65 -31674.86 63479.71 0.000000e+00 63480.24 0.000000e+00
## 77 TVMe 67 -31673.13 63480.26 0.000000e+00 63480.82 0.000000e+00
## 69 TIM3e 66 -31695.21 63522.42 0.000000e+00 63522.96 0.000000e+00
## 17 TrNe 65 -31696.40 63522.80 0.000000e+00 63523.32 0.000000e+00
## 53 TIM1e 66 -31696.40 63524.80 0.000000e+00 63525.34 0.000000e+00
## 45 TPM3 65 -31737.58 63605.17 0.000000e+00 63605.69 0.000000e+00
## 9 K80 64 -31738.74 63605.47 0.000000e+00 63605.98 0.000000e+00
## 25 TPM1 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 29 K81 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 5 F81 66 -32078.43 64288.86 0.000000e+00 64289.40 0.000000e+00
## 4 JC+G(4)+I 65 -32223.44 64576.88 0.000000e+00 64577.40 0.000000e+00
## 3 JC+G(4) 64 -32237.07 64602.14 0.000000e+00 64602.65 0.000000e+00
## 2 JC+I 64 -32237.33 64602.66 0.000000e+00 64603.17 0.000000e+00
## 1 JC 63 -32775.40 65676.79 0.000000e+00 65677.29 0.000000e+00
## BIC
## 84 61157.25
## 52 61142.14
## 92 61166.27
## 44 61143.36
## 76 61151.39
## 68 61152.35
## 16 61137.58
## 24 61146.80
## 36 61146.83
## 60 61156.07
## 51 61145.77
## 83 61161.64
## 43 61147.17
## 75 61155.38
## 91 61171.32
## 15 61140.50
## 67 61156.86
## 35 61149.86
## 23 61150.14
## 59 61159.49
## 82 61272.63
## 90 61280.40
## 42 61261.53
## 66 61269.32
## 50 61267.14
## 74 61275.74
## 14 61264.33
## 22 61272.96
## 34 61273.77
## 58 61282.41
## 89 62621.84
## 65 62606.99
## 81 62622.69
## 41 62607.80
## 73 62664.93
## 21 62658.29
## 57 62667.99
## 49 62665.76
## 13 62659.09
## 33 62668.78
## 88 62704.18
## 64 62690.93
## 87 62729.74
## 63 62716.18
## 72 62739.66
## 20 62735.60
## 56 62745.28
## 86 62763.30
## 80 62766.96
## 62 62753.45
## 40 62753.99
## 71 62758.82
## 19 62754.07
## 55 62763.74
## 79 62774.03
## 39 62760.90
## 48 62793.14
## 12 62789.39
## 28 62799.04
## 32 62799.04
## 47 62794.69
## 11 62790.43
## 27 62800.04
## 31 62800.04
## 70 62820.47
## 18 62820.14
## 54 62829.83
## 78 62847.57
## 38 62837.60
## 46 62893.82
## 10 62893.22
## 26 62902.91
## 30 62902.91
## 8 63642.09
## 7 63655.61
## 6 63667.25
## 61 63905.00
## 85 63920.83
## 37 63980.58
## 77 63996.54
## 69 64030.99
## 17 64023.66
## 53 64033.37
## 45 64106.03
## 9 64098.64
## 25 64108.34
## 29 64108.34
## 5 64797.44
## 4 65077.75
## 3 65095.31
## 2 65095.83
## 1 66162.25mySequences_gr_ext_5_modelTest[order(mySequences_gr_ext_5_modelTest$BIC), ]## Model df logLik AIC AICw AICc AICcw
## 16 HKY+G(4)+I 69 -30233.94 60605.89 4.597245e-02 60606.48 4.679408e-02
## 15 HKY+G(4) 68 -30240.26 60616.52 2.262507e-04 60617.09 2.322516e-04
## 52 TPM3u+G(4)+I 70 -30231.37 60602.74 2.215058e-01 60603.35 2.235370e-01
## 44 TPM2u+G(4)+I 70 -30231.98 60603.96 1.204924e-01 60604.57 1.215973e-01
## 51 TPM3u+G(4) 69 -30238.04 60614.08 7.665745e-04 60614.67 7.802749e-04
## 24 TrN+G(4)+I 70 -30233.70 60607.41 2.150824e-02 60608.02 2.170547e-02
## 36 TPM1u+G(4)+I 70 -30233.72 60607.43 2.122298e-02 60608.04 2.141759e-02
## 43 TPM2u+G(4) 69 -30238.74 60615.48 3.793342e-04 60616.07 3.861137e-04
## 35 TPM1u+G(4) 69 -30240.09 60618.17 9.879058e-05 60618.77 1.005562e-04
## 23 TrN+G(4) 69 -30240.22 60618.45 8.625433e-05 60619.04 8.779589e-05
## 76 TIM3+G(4)+I 71 -30231.15 60604.29 1.022371e-01 60604.92 1.022798e-01
## 68 TIM2+G(4)+I 71 -30231.62 60605.25 6.335246e-02 60605.87 6.337894e-02
## 75 TIM3+G(4) 70 -30237.99 60615.99 2.946165e-04 60616.60 2.973180e-04
## 60 TIM1+G(4)+I 71 -30233.48 60608.97 9.867728e-03 60609.59 9.871852e-03
## 67 TIM2+G(4) 70 -30238.73 60617.46 1.408620e-04 60618.07 1.421537e-04
## 84 TVM+G(4)+I 72 -30229.22 60602.44 2.576621e-01 60603.09 2.555028e-01
## 59 TIM1+G(4) 70 -30240.05 60620.10 3.778567e-05 60620.70 3.813215e-05
## 83 TVM+G(4) 71 -30236.27 60614.54 6.094845e-04 60615.16 6.097392e-04
## 92 GTR+G(4)+I 73 -30228.88 60603.76 1.333119e-01 60604.42 1.310159e-01
## 91 GTR+G(4) 72 -30236.26 60616.51 2.268411e-04 60617.16 2.249401e-04
## 42 TPM2u+I 69 -30295.92 60729.84 5.576489e-29 60730.43 5.676154e-29
## 14 HKY+I 68 -30302.17 60740.35 2.918886e-31 60740.92 2.996305e-31
## 50 TPM3u+I 69 -30298.72 60735.45 3.377990e-30 60736.04 3.438362e-30
## 66 TIM2+I 70 -30294.96 60729.92 5.356339e-29 60730.53 5.405454e-29
## 82 TVM+I 71 -30291.76 60725.53 4.827230e-28 60726.15 4.829248e-28
## 22 TrN+I 69 -30301.63 60741.27 1.842596e-31 60741.86 1.875528e-31
## 34 TPM1u+I 69 -30302.04 60742.08 1.225962e-31 60742.67 1.247873e-31
## 74 TIM3+I 70 -30298.17 60736.35 2.156340e-30 60736.96 2.176113e-30
## 90 GTR+I 72 -30290.79 60725.59 4.676748e-28 60726.23 4.637556e-28
## 58 TIM1+I 70 -30301.51 60743.02 7.689664e-32 60743.62 7.760176e-32
## 65 TIM2 69 -30968.65 62075.30 3.833949e-321 62075.89 3.903119e-321
## 41 TPM2u 68 -30973.91 62083.82 5.434722e-323 62084.39 5.434722e-323
## 89 GTR 71 -30966.37 62074.74 5.069114e-321 62075.37 5.074054e-321
## 81 TVM 70 -30971.65 62083.30 6.916919e-323 62083.91 6.916919e-323
## 21 TrN 68 -30999.16 62134.31 0.000000e+00 62134.88 0.000000e+00
## 13 HKY 67 -31004.41 62142.81 0.000000e+00 62143.37 0.000000e+00
## 73 TIM3 69 -30997.62 62133.24 0.000000e+00 62133.83 0.000000e+00
## 49 TPM3u 68 -31002.89 62141.77 0.000000e+00 62142.35 0.000000e+00
## 57 TIM1 69 -30999.15 62136.30 0.000000e+00 62136.89 0.000000e+00
## 33 TPM1u 68 -31004.40 62144.80 0.000000e+00 62145.37 0.000000e+00
## 64 TIM2e+G(4)+I 68 -31015.47 62166.95 0.000000e+00 62167.52 0.000000e+00
## 88 SYM+G(4)+I 70 -31012.39 62164.78 0.000000e+00 62165.39 0.000000e+00
## 63 TIM2e+G(4) 67 -31032.95 62199.91 0.000000e+00 62200.46 0.000000e+00
## 87 SYM+G(4) 69 -31030.03 62198.05 0.000000e+00 62198.64 0.000000e+00
## 20 TrNe+G(4)+I 67 -31042.66 62219.32 0.000000e+00 62219.88 0.000000e+00
## 72 TIM3e+G(4)+I 68 -31039.84 62215.68 0.000000e+00 62216.25 0.000000e+00
## 56 TIM1e+G(4)+I 68 -31042.65 62221.30 0.000000e+00 62221.87 0.000000e+00
## 62 TIM2e+I 67 -31051.59 62237.18 0.000000e+00 62237.73 0.000000e+00
## 40 TPM2+G(4)+I 67 -31051.86 62237.71 0.000000e+00 62238.27 0.000000e+00
## 19 TrNe+G(4) 66 -31056.75 62245.50 0.000000e+00 62246.04 0.000000e+00
## 71 TIM3e+G(4) 67 -31054.27 62242.54 0.000000e+00 62243.10 0.000000e+00
## 39 TPM2+G(4) 66 -31060.17 62252.33 0.000000e+00 62252.87 0.000000e+00
## 86 SYM+I 69 -31046.80 62231.61 0.000000e+00 62232.20 0.000000e+00
## 55 TIM1e+G(4) 67 -31056.73 62247.46 0.000000e+00 62248.02 0.000000e+00
## 80 TVMe+G(4)+I 69 -31048.64 62235.27 0.000000e+00 62235.87 0.000000e+00
## 79 TVMe+G(4) 68 -31057.02 62250.04 0.000000e+00 62250.62 0.000000e+00
## 12 K80+G(4)+I 66 -31074.41 62280.82 0.000000e+00 62281.36 0.000000e+00
## 11 K80+G(4) 65 -31079.78 62289.57 0.000000e+00 62290.09 0.000000e+00
## 48 TPM3+G(4)+I 67 -31071.43 62276.86 0.000000e+00 62277.41 0.000000e+00
## 47 TPM3+G(4) 66 -31077.06 62286.12 0.000000e+00 62286.66 0.000000e+00
## 28 TPM1+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 32 K81+G(4)+I 67 -31074.38 62282.76 0.000000e+00 62283.32 0.000000e+00
## 27 TPM1+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 31 K81+G(4) 66 -31079.74 62291.47 0.000000e+00 62292.01 0.000000e+00
## 18 TrNe+I 66 -31089.78 62311.56 0.000000e+00 62312.10 0.000000e+00
## 70 TIM3e+I 67 -31085.09 62304.19 0.000000e+00 62304.75 0.000000e+00
## 54 TIM1e+I 67 -31089.78 62313.55 0.000000e+00 62314.11 0.000000e+00
## 38 TPM2+I 66 -31098.51 62329.02 0.000000e+00 62329.57 0.000000e+00
## 78 TVMe+I 68 -31093.79 62323.58 0.000000e+00 62324.16 0.000000e+00
## 10 K80+I 65 -31131.18 62392.35 0.000000e+00 62392.88 0.000000e+00
## 46 TPM3+I 66 -31126.63 62385.25 0.000000e+00 62385.79 0.000000e+00
## 26 TPM1+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 30 K81+I 66 -31131.17 62394.34 0.000000e+00 62394.88 0.000000e+00
## 8 F81+G(4)+I 68 -31491.05 63118.10 0.000000e+00 63118.68 0.000000e+00
## 7 F81+G(4) 67 -31502.67 63139.33 0.000000e+00 63139.89 0.000000e+00
## 6 F81+I 67 -31508.49 63150.97 0.000000e+00 63151.53 0.000000e+00
## 61 TIM2e 66 -31632.21 63396.43 0.000000e+00 63396.97 0.000000e+00
## 85 SYM 68 -31630.42 63396.84 0.000000e+00 63397.42 0.000000e+00
## 37 TPM2 65 -31674.86 63479.71 0.000000e+00 63480.24 0.000000e+00
## 77 TVMe 67 -31673.13 63480.26 0.000000e+00 63480.82 0.000000e+00
## 17 TrNe 65 -31696.40 63522.80 0.000000e+00 63523.32 0.000000e+00
## 69 TIM3e 66 -31695.21 63522.42 0.000000e+00 63522.96 0.000000e+00
## 53 TIM1e 66 -31696.40 63524.80 0.000000e+00 63525.34 0.000000e+00
## 9 K80 64 -31738.74 63605.47 0.000000e+00 63605.98 0.000000e+00
## 45 TPM3 65 -31737.58 63605.17 0.000000e+00 63605.69 0.000000e+00
## 25 TPM1 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 29 K81 65 -31738.74 63607.47 0.000000e+00 63608.00 0.000000e+00
## 5 F81 66 -32078.43 64288.86 0.000000e+00 64289.40 0.000000e+00
## 4 JC+G(4)+I 65 -32223.44 64576.88 0.000000e+00 64577.40 0.000000e+00
## 3 JC+G(4) 64 -32237.07 64602.14 0.000000e+00 64602.65 0.000000e+00
## 2 JC+I 64 -32237.33 64602.66 0.000000e+00 64603.17 0.000000e+00
## 1 JC 63 -32775.40 65676.79 0.000000e+00 65677.29 0.000000e+00
## BIC
## 16 61137.58
## 15 61140.50
## 52 61142.14
## 44 61143.36
## 51 61145.77
## 24 61146.80
## 36 61146.83
## 43 61147.17
## 35 61149.86
## 23 61150.14
## 76 61151.39
## 68 61152.35
## 75 61155.38
## 60 61156.07
## 67 61156.86
## 84 61157.25
## 59 61159.49
## 83 61161.64
## 92 61166.27
## 91 61171.32
## 42 61261.53
## 14 61264.33
## 50 61267.14
## 66 61269.32
## 82 61272.63
## 22 61272.96
## 34 61273.77
## 74 61275.74
## 90 61280.40
## 58 61282.41
## 65 62606.99
## 41 62607.80
## 89 62621.84
## 81 62622.69
## 21 62658.29
## 13 62659.09
## 73 62664.93
## 49 62665.76
## 57 62667.99
## 33 62668.78
## 64 62690.93
## 88 62704.18
## 63 62716.18
## 87 62729.74
## 20 62735.60
## 72 62739.66
## 56 62745.28
## 62 62753.45
## 40 62753.99
## 19 62754.07
## 71 62758.82
## 39 62760.90
## 86 62763.30
## 55 62763.74
## 80 62766.96
## 79 62774.03
## 12 62789.39
## 11 62790.43
## 48 62793.14
## 47 62794.69
## 28 62799.04
## 32 62799.04
## 27 62800.04
## 31 62800.04
## 18 62820.14
## 70 62820.47
## 54 62829.83
## 38 62837.60
## 78 62847.57
## 10 62893.22
## 46 62893.82
## 26 62902.91
## 30 62902.91
## 8 63642.09
## 7 63655.61
## 6 63667.25
## 61 63905.00
## 85 63920.83
## 37 63980.58
## 77 63996.54
## 17 64023.66
## 69 64030.99
## 53 64033.37
## 9 64098.64
## 45 64106.03
## 25 64108.34
## 29 64108.34
## 5 64797.44
## 4 65077.75
## 3 65095.31
## 2 65095.83
## 1 66162.25Meilleur modele: TPM3u+G(4)+I
env$`TPM3u+G(4)+I`## pml(tree = `tree_TPM3u+G(4)+I`, data = data, bf = c(0.305879919520129,
## 0.277448712886181, 0.150392057313702, 0.266279310279987), Q = c(0.620577836420439,
## 16.6238593112725, 1, 0.620577836420439, 16.6238593112725, 1),
## model = "TPM3u", inv = 0.552749390092391, k = 4, shape = 1.18214235444543)Construction d’arbres
# Matrice de distance
mySequences_align_gr_ext_5 = dist.logDet(mySequences_align_gr_ext_5_phangorn)
# Construction arbre NJ
treeNJ_gr_ext_5 <- NJ(mySequences_align_gr_ext_5)
# Visualisation
plot(treeNJ_gr_ext_5, main="Arbre NJ Groupe externe 5")
Integration des parametres
fit_gr_ext_5 = pml(treeNJ_gr_ext_5, data=mySequences_align_gr_ext_5_phangorn)
fitTPM3u_gr_ext_5 <- update(fit_gr_ext_5, model="TPM3u", k=4, inv=0.552855466228451, shape=1.18392191329267)
fitTPM3u_gr_ext_5 <- optim.pml(fitTPM3u_gr_ext_5, model="TPM3u", optInv=TRUE, optGamma=TRUE, optShape = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_gr_ext_5 = bootstrap.pml(fitTPM3u_gr_ext_5, multicore=TRUE, mc.cores=10, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitTPM3u_gr_ext_5$tree), bs_gr_ext_5, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")
AA
Alignement
mySequences_align_aa_gr_ext_5 = AlignTranslation(Sequences_groupe_externe_5,
sense = "+",
readingFrame = NA,
type = "AAStringSet",
gapOpening = c(-18,-16),
gapExtension = c(-2,-1),
geneticCode = my_g_table)## Determining distance matrix based on shared 6-mers:
## ================================================================================
##
## Time difference of 0 secs
##
## Clustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Aligning Sequences:
## ================================================================================
##
## Time difference of 1.12 secs
##
## Iteration 1 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.15 secs
##
## Iteration 2 of 2:
##
## Determining distance matrix based on alignment:
## ================================================================================
##
## Time difference of 0 secs
##
## Reclustering into groups by similarity:
## ================================================================================
##
## Time difference of 0 secs
##
## Realigning Sequences:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Refining the alignment:
## ================================================================================
##
## Time difference of 1.76 secsConversion
mySequences_align_aa_gr_ext_5_ape = as.AAbin(mySequences_align_aa_gr_ext_5)
mySequences_align_aa_gr_ext_5_phangorn = as.phyDat.AAbin(mySequences_align_aa_gr_ext_5_ape, type = "AA")## Warning in phyDat.AA(data, return.index = return.index, ...): Found unknown
## characters (not supplied in levels). Deleted sites with unknown states.Recherche du meilleur modele
mySequences_align_aa_gr_ext_5_modeltest = phangorn::modelTest(mySequences_align_aa_gr_ext_5_phangorn, model = c("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT", "RtREV", "HIVw", "HIVb", "FLU", "Blosum62", "Dayhoff_DCMut", "JTT_DCMut"))## Model df logLik AIC BIC
## WAG 63 -29719.28 59564.56 60002.67
## WAG+I 64 -29692.37 59512.74 59957.81
## WAG+G(4) 64 -29687.28 59502.55 59947.62
## WAG+G(4)+I 65 -29687.29 59504.58 59956.6
## JTT 63 -29599.93 59325.86 59763.98
## JTT+I 64 -29549.29 59226.58 59671.65
## JTT+G(4) 64 -29542.48 59212.95 59658.02
## JTT+G(4)+I 65 -29542.49 59214.99 59667.01
## LG 63 -29752.74 59631.49 60069.6
## LG+I 64 -29696.06 59520.13 59965.2
## LG+G(4) 64 -29684.48 59496.96 59942.03
## LG+G(4)+I 65 -29684.49 59498.97 59950.99
## Dayhoff 63 -30401.82 60929.64 61367.75
## Dayhoff+I 64 -30401.82 60931.64 61376.7
## Dayhoff+G(4) 64 -30402.21 60932.41 61377.48
## Dayhoff+G(4)+I 65 -30402.21 60934.41 61386.43
## cpREV 63 -29824.29 59774.59 60212.7
## cpREV+I 64 -29747.74 59623.49 60068.56
## cpREV+G(4) 64 -29743.66 59615.33 60060.39
## cpREV+G(4)+I 65 -29743.36 59616.72 60068.74
## mtmam 63 -30756.67 61639.35 62077.46
## mtmam+I 64 -30716.52 61561.05 62006.11
## mtmam+G(4) 64 -30715.03 61558.07 62003.13
## mtmam+G(4)+I 65 -30715.03 61560.05 62012.07
## mtArt 63 -29955.98 60037.97 60476.08
## mtArt+I 64 -29775.88 59679.76 60124.83
## mtArt+G(4) 64 -29727.75 59583.5 60028.57
## mtArt+G(4)+I 65 -29728.06 59586.12 60038.14
## MtZoa 63 -29889.03 59904.06 60342.18
## MtZoa+I 64 -29752.38 59632.76 60077.82
## MtZoa+G(4) 64 -29722.6 59573.19 60018.26
## MtZoa+G(4)+I 65 -29722.89 59575.77 60027.79
## mtREV24 63 -29416.38 58958.75 59396.87
## mtREV24+I 64 -29312.73 58753.47 59198.53
## mtREV24+G(4) 64 -29277.86 58683.73 59128.79
## mtREV24+G(4)+I 65 -29278.56 58687.11 59139.13
## VT 63 -29823.35 59772.69 60210.81
## VT+I 64 -29766.21 59660.42 60105.48
## VT+G(4) 64 -29742.01 59612.03 60057.09
## VT+G(4)+I 65 -29741.98 59613.97 60065.99
## RtREV 63 -29537.53 59201.06 59639.17
## RtREV+I 64 -29492.31 59112.63 59557.69
## RtREV+G(4) 64 -29482.59 59093.17 59538.24
## RtREV+G(4)+I 65 -29482.59 59095.18 59547.2
## HIVw 63 -30422.04 60970.09 61408.2
## HIVw+I 64 -30236.56 60601.13 61046.19
## HIVw+G(4) 64 -30209.78 60547.56 60992.63
## HIVw+G(4)+I 65 -30210.73 60551.46 61003.48
## HIVb 63 -29992.79 60111.59 60549.7
## HIVb+I 64 -29865.06 59858.11 60303.18
## HIVb+G(4) 64 -29854.96 59837.93 60282.99
## HIVb+G(4)+I 65 -29854.39 59838.79 60290.81
## FLU 63 -29565.76 59257.52 59695.63
## FLU+I 64 -29474.33 59076.66 59521.73
## FLU+G(4) 64 -30302.69 60733.38 61178.44
## FLU+G(4)+I 65 -29468.82 59067.65 59519.67
## Blosum62 63 -29757.08 59640.17 60078.28
## Blosum62+I 64 -29754.67 59637.34 60082.41
## Blosum62+G(4) 64 -29751.49 59630.97 60076.04
## Blosum62+G(4)+I 65 -29751.51 59633.02 60085.04
## Dayhoff_DCMut 63 -30398.14 60922.28 61360.39
## Dayhoff_DCMut+I 64 -30398.14 60924.28 61369.35
## Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 61370.15
## Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 61379.1
## JTT_DCMut 63 -29616.99 59359.98 59798.09
## JTT_DCMut+I 64 -29566.38 59260.76 59705.83
## JTT_DCMut+G(4) 64 -29559.78 59247.55 59692.62
## JTT_DCMut+G(4)+I 65 -29559.79 59249.59 59701.61Trouver le meilleur modele
env <- attr(mySequences_align_aa_gr_ext_5_modeltest, "env")
ls(env=env)## [1] "Blosum62" "Blosum62+G(4)"
## [3] "Blosum62+G(4)+I" "Blosum62+I"
## [5] "cpREV" "cpREV+G(4)"
## [7] "cpREV+G(4)+I" "cpREV+I"
## [9] "data" "Dayhoff"
## [11] "Dayhoff_DCMut" "Dayhoff_DCMut+G(4)"
## [13] "Dayhoff_DCMut+G(4)+I" "Dayhoff_DCMut+I"
## [15] "Dayhoff+G(4)" "Dayhoff+G(4)+I"
## [17] "Dayhoff+I" "FLU"
## [19] "FLU+G(4)" "FLU+G(4)+I"
## [21] "FLU+I" "HIVb"
## [23] "HIVb+G(4)" "HIVb+G(4)+I"
## [25] "HIVb+I" "HIVw"
## [27] "HIVw+G(4)" "HIVw+G(4)+I"
## [29] "HIVw+I" "JTT"
## [31] "JTT_DCMut" "JTT_DCMut+G(4)"
## [33] "JTT_DCMut+G(4)+I" "JTT_DCMut+I"
## [35] "JTT+G(4)" "JTT+G(4)+I"
## [37] "JTT+I" "LG"
## [39] "LG+G(4)" "LG+G(4)+I"
## [41] "LG+I" "mtArt"
## [43] "mtArt+G(4)" "mtArt+G(4)+I"
## [45] "mtArt+I" "mtmam"
## [47] "mtmam+G(4)" "mtmam+G(4)+I"
## [49] "mtmam+I" "mtREV24"
## [51] "mtREV24+G(4)" "mtREV24+G(4)+I"
## [53] "mtREV24+I" "MtZoa"
## [55] "MtZoa+G(4)" "MtZoa+G(4)+I"
## [57] "MtZoa+I" "RtREV"
## [59] "RtREV+G(4)" "RtREV+G(4)+I"
## [61] "RtREV+I" "tree_Blosum62"
## [63] "tree_Blosum62+G(4)" "tree_Blosum62+G(4)+I"
## [65] "tree_Blosum62+I" "tree_cpREV"
## [67] "tree_cpREV+G(4)" "tree_cpREV+G(4)+I"
## [69] "tree_cpREV+I" "tree_Dayhoff"
## [71] "tree_Dayhoff_DCMut" "tree_Dayhoff_DCMut+G(4)"
## [73] "tree_Dayhoff_DCMut+G(4)+I" "tree_Dayhoff_DCMut+I"
## [75] "tree_Dayhoff+G(4)" "tree_Dayhoff+G(4)+I"
## [77] "tree_Dayhoff+I" "tree_FLU"
## [79] "tree_FLU+G(4)" "tree_FLU+G(4)+I"
## [81] "tree_FLU+I" "tree_HIVb"
## [83] "tree_HIVb+G(4)" "tree_HIVb+G(4)+I"
## [85] "tree_HIVb+I" "tree_HIVw"
## [87] "tree_HIVw+G(4)" "tree_HIVw+G(4)+I"
## [89] "tree_HIVw+I" "tree_JTT"
## [91] "tree_JTT_DCMut" "tree_JTT_DCMut+G(4)"
## [93] "tree_JTT_DCMut+G(4)+I" "tree_JTT_DCMut+I"
## [95] "tree_JTT+G(4)" "tree_JTT+G(4)+I"
## [97] "tree_JTT+I" "tree_LG"
## [99] "tree_LG+G(4)" "tree_LG+G(4)+I"
## [101] "tree_LG+I" "tree_mtArt"
## [103] "tree_mtArt+G(4)" "tree_mtArt+G(4)+I"
## [105] "tree_mtArt+I" "tree_mtmam"
## [107] "tree_mtmam+G(4)" "tree_mtmam+G(4)+I"
## [109] "tree_mtmam+I" "tree_mtREV24"
## [111] "tree_mtREV24+G(4)" "tree_mtREV24+G(4)+I"
## [113] "tree_mtREV24+I" "tree_MtZoa"
## [115] "tree_MtZoa+G(4)" "tree_MtZoa+G(4)+I"
## [117] "tree_MtZoa+I" "tree_RtREV"
## [119] "tree_RtREV+G(4)" "tree_RtREV+G(4)+I"
## [121] "tree_RtREV+I" "tree_VT"
## [123] "tree_VT+G(4)" "tree_VT+G(4)+I"
## [125] "tree_VT+I" "tree_WAG"
## [127] "tree_WAG+G(4)" "tree_WAG+G(4)+I"
## [129] "tree_WAG+I" "VT"
## [131] "VT+G(4)" "VT+G(4)+I"
## [133] "VT+I" "WAG"
## [135] "WAG+G(4)" "WAG+G(4)+I"
## [137] "WAG+I"mySequences_align_aa_gr_ext_5_modeltest[order(mySequences_align_aa_gr_ext_5_modeltest$AIC), ]## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 64 -29277.86 58683.73 8.443734e-01 58684.81
## 36 mtREV24+G(4)+I 65 -29278.56 58687.11 1.556266e-01 58688.23
## 34 mtREV24+I 64 -29312.73 58753.47 6.070336e-16 58754.55
## 33 mtREV24 63 -29416.38 58958.75 1.604746e-60 58959.80
## 56 FLU+G(4)+I 65 -29468.82 59067.65 3.623119e-84 59068.77
## 54 FLU+I 64 -29474.33 59076.66 4.000297e-86 59077.75
## 43 RtREV+G(4) 64 -29482.59 59093.17 1.039652e-89 59094.26
## 44 RtREV+G(4)+I 65 -29482.59 59095.18 3.803450e-90 59096.30
## 42 RtREV+I 64 -29492.31 59112.63 6.194778e-94 59113.71
## 41 RtREV 63 -29537.53 59201.06 3.892388e-113 59202.11
## 7 JTT+G(4) 64 -29542.48 59212.95 1.016163e-115 59214.04
## 8 JTT+G(4)+I 65 -29542.49 59214.99 3.671867e-116 59216.11
## 6 JTT+I 64 -29549.29 59226.58 1.116155e-118 59227.66
## 67 JTT_DCMut+G(4) 64 -29559.78 59247.55 3.114891e-123 59248.64
## 68 JTT_DCMut+G(4)+I 65 -29559.79 59249.59 1.125500e-123 59250.71
## 53 FLU 63 -29565.76 59257.52 2.137399e-125 59258.57
## 66 JTT_DCMut+I 64 -29566.38 59260.76 4.214858e-126 59261.85
## 5 JTT 63 -29599.93 59325.86 3.078524e-140 59326.92
## 65 JTT_DCMut 63 -29616.99 59359.98 1.204319e-147 59361.03
## 11 LG+G(4) 64 -29684.48 59496.96 2.159778e-177 59498.05
## 12 LG+G(4)+I 65 -29684.49 59498.97 7.921894e-178 59500.09
## 3 WAG+G(4) 64 -29687.28 59502.55 1.322408e-178 59503.64
## 4 WAG+G(4)+I 65 -29687.29 59504.58 4.785470e-179 59505.70
## 2 WAG+I 64 -29692.37 59512.74 8.091514e-181 59513.83
## 10 LG+I 64 -29696.06 59520.13 2.014807e-182 59521.21
## 1 WAG 63 -29719.28 59564.56 4.534831e-192 59565.61
## 31 MtZoa+G(4) 64 -29722.60 59573.19 6.047715e-194 59574.28
## 32 MtZoa+G(4)+I 65 -29722.89 59575.77 1.664165e-194 59576.89
## 27 mtArt+G(4) 64 -29727.75 59583.50 3.488603e-196 59584.59
## 28 mtArt+G(4)+I 65 -29728.06 59586.12 9.447127e-197 59587.23
## 39 VT+G(4) 64 -29742.01 59612.03 2.231969e-202 59613.11
## 40 VT+G(4)+I 65 -29741.98 59613.97 8.464233e-203 59615.09
## 19 cpREV+G(4) 64 -29743.66 59615.33 4.292618e-203 59616.41
## 20 cpREV+G(4)+I 65 -29743.36 59616.72 2.134880e-203 59617.84
## 18 cpREV+I 64 -29747.74 59623.49 7.242854e-205 59624.57
## 59 Blosum62+G(4) 64 -29751.49 59630.97 1.718260e-206 59632.06
## 9 LG 63 -29752.74 59631.49 1.327548e-206 59632.54
## 30 MtZoa+I 64 -29752.38 59632.76 7.041167e-207 59633.84
## 60 Blosum62+G(4)+I 65 -29751.51 59633.02 6.167908e-207 59634.14
## 58 Blosum62+I 64 -29754.67 59637.34 7.099579e-208 59638.43
## 57 Blosum62 63 -29757.08 59640.17 1.730959e-208 59641.22
## 38 VT+I 64 -29766.21 59660.42 6.931260e-213 59661.50
## 26 mtArt+I 64 -29775.88 59679.76 4.365891e-217 59680.85
## 37 VT 63 -29823.35 59772.69 2.888224e-237 59773.74
## 17 cpREV 63 -29824.29 59774.59 1.119339e-237 59775.64
## 51 HIVb+G(4) 64 -29854.96 59837.93 1.973936e-251 59839.01
## 52 HIVb+G(4)+I 65 -29854.39 59838.79 1.283383e-251 59839.91
## 50 HIVb+I 64 -29865.06 59858.11 8.168730e-256 59859.20
## 29 MtZoa 63 -29889.03 59904.06 8.591882e-266 59905.11
## 25 mtArt 63 -29955.98 60037.97 7.196560e-295 60039.02
## 49 HIVb 63 -29992.79 60111.59 7.422148e-311 60112.64
## 47 HIVw+G(4) 64 -30209.78 60547.56 0.000000e+00 60548.65
## 48 HIVw+G(4)+I 65 -30210.73 60551.46 0.000000e+00 60552.58
## 46 HIVw+I 64 -30236.56 60601.13 0.000000e+00 60602.21
## 55 FLU+G(4) 64 -30302.69 60733.38 0.000000e+00 60734.46
## 61 Dayhoff_DCMut 63 -30398.14 60922.28 0.000000e+00 60923.33
## 62 Dayhoff_DCMut+I 64 -30398.14 60924.28 0.000000e+00 60925.37
## 63 Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 0.000000e+00 60926.16
## 64 Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 0.000000e+00 60928.20
## 13 Dayhoff 63 -30401.82 60929.64 0.000000e+00 60930.69
## 14 Dayhoff+I 64 -30401.82 60931.64 0.000000e+00 60932.72
## 15 Dayhoff+G(4) 64 -30402.21 60932.41 0.000000e+00 60933.50
## 16 Dayhoff+G(4)+I 65 -30402.21 60934.41 0.000000e+00 60935.53
## 45 HIVw 63 -30422.04 60970.09 0.000000e+00 60971.14
## 23 mtmam+G(4) 64 -30715.03 61558.07 0.000000e+00 61559.15
## 24 mtmam+G(4)+I 65 -30715.03 61560.05 0.000000e+00 61561.17
## 22 mtmam+I 64 -30716.52 61561.05 0.000000e+00 61562.13
## 21 mtmam 63 -30756.67 61639.35 0.000000e+00 61640.40
## AICcw BIC
## 35 8.465957e-01 59128.79
## 36 1.534043e-01 59139.13
## 34 6.086313e-16 59198.53
## 33 1.636140e-60 59396.87
## 56 3.571382e-84 59519.67
## 54 4.010825e-86 59521.73
## 43 1.042388e-89 59538.24
## 44 3.749138e-90 59547.20
## 42 6.211082e-94 59557.69
## 41 3.968536e-113 59639.17
## 7 1.018837e-115 59658.02
## 8 3.619434e-116 59667.01
## 6 1.119092e-118 59671.65
## 67 3.123089e-123 59692.62
## 68 1.109428e-123 59701.61
## 53 2.179213e-125 59695.63
## 66 4.225951e-126 59705.83
## 5 3.138750e-140 59763.98
## 65 1.227880e-147 59798.09
## 11 2.165462e-177 59942.03
## 12 7.808773e-178 59950.99
## 3 1.325889e-178 59947.62
## 4 4.717135e-179 59956.60
## 2 8.112810e-181 59957.81
## 10 2.020110e-182 59965.20
## 1 4.623548e-192 60002.67
## 31 6.063632e-194 60018.26
## 32 1.640402e-194 60027.79
## 27 3.497785e-196 60028.57
## 28 9.312226e-197 60038.14
## 39 2.237843e-202 60057.09
## 40 8.343368e-203 60065.99
## 19 4.303916e-203 60060.39
## 20 2.104395e-203 60068.74
## 18 7.261916e-205 60068.56
## 59 1.722782e-206 60076.04
## 9 1.353519e-206 60069.60
## 30 7.059698e-207 60077.82
## 60 6.079833e-207 60085.04
## 58 7.118264e-208 60082.41
## 57 1.764822e-208 60078.28
## 38 6.949503e-213 60105.48
## 26 4.377381e-217 60124.83
## 37 2.944727e-237 60210.81
## 17 1.141237e-237 60212.70
## 51 1.979131e-251 60282.99
## 52 1.265056e-251 60290.81
## 50 8.190229e-256 60303.18
## 29 8.759968e-266 60342.18
## 25 7.337348e-295 60476.08
## 49 7.567350e-311 60549.70
## 47 0.000000e+00 60992.63
## 48 0.000000e+00 61003.48
## 46 0.000000e+00 61046.19
## 55 0.000000e+00 61178.44
## 61 0.000000e+00 61360.39
## 62 0.000000e+00 61369.35
## 63 0.000000e+00 61370.15
## 64 0.000000e+00 61379.10
## 13 0.000000e+00 61367.75
## 14 0.000000e+00 61376.70
## 15 0.000000e+00 61377.48
## 16 0.000000e+00 61386.43
## 45 0.000000e+00 61408.20
## 23 0.000000e+00 62003.13
## 24 0.000000e+00 62012.07
## 22 0.000000e+00 62006.11
## 21 0.000000e+00 62077.46mySequences_align_aa_gr_ext_5_modeltest[order(mySequences_align_aa_gr_ext_5_modeltest$BIC), ]## Model df logLik AIC AICw AICc
## 35 mtREV24+G(4) 64 -29277.86 58683.73 8.443734e-01 58684.81
## 36 mtREV24+G(4)+I 65 -29278.56 58687.11 1.556266e-01 58688.23
## 34 mtREV24+I 64 -29312.73 58753.47 6.070336e-16 58754.55
## 33 mtREV24 63 -29416.38 58958.75 1.604746e-60 58959.80
## 56 FLU+G(4)+I 65 -29468.82 59067.65 3.623119e-84 59068.77
## 54 FLU+I 64 -29474.33 59076.66 4.000297e-86 59077.75
## 43 RtREV+G(4) 64 -29482.59 59093.17 1.039652e-89 59094.26
## 44 RtREV+G(4)+I 65 -29482.59 59095.18 3.803450e-90 59096.30
## 42 RtREV+I 64 -29492.31 59112.63 6.194778e-94 59113.71
## 41 RtREV 63 -29537.53 59201.06 3.892388e-113 59202.11
## 7 JTT+G(4) 64 -29542.48 59212.95 1.016163e-115 59214.04
## 8 JTT+G(4)+I 65 -29542.49 59214.99 3.671867e-116 59216.11
## 6 JTT+I 64 -29549.29 59226.58 1.116155e-118 59227.66
## 67 JTT_DCMut+G(4) 64 -29559.78 59247.55 3.114891e-123 59248.64
## 53 FLU 63 -29565.76 59257.52 2.137399e-125 59258.57
## 68 JTT_DCMut+G(4)+I 65 -29559.79 59249.59 1.125500e-123 59250.71
## 66 JTT_DCMut+I 64 -29566.38 59260.76 4.214858e-126 59261.85
## 5 JTT 63 -29599.93 59325.86 3.078524e-140 59326.92
## 65 JTT_DCMut 63 -29616.99 59359.98 1.204319e-147 59361.03
## 11 LG+G(4) 64 -29684.48 59496.96 2.159778e-177 59498.05
## 3 WAG+G(4) 64 -29687.28 59502.55 1.322408e-178 59503.64
## 12 LG+G(4)+I 65 -29684.49 59498.97 7.921894e-178 59500.09
## 4 WAG+G(4)+I 65 -29687.29 59504.58 4.785470e-179 59505.70
## 2 WAG+I 64 -29692.37 59512.74 8.091514e-181 59513.83
## 10 LG+I 64 -29696.06 59520.13 2.014807e-182 59521.21
## 1 WAG 63 -29719.28 59564.56 4.534831e-192 59565.61
## 31 MtZoa+G(4) 64 -29722.60 59573.19 6.047715e-194 59574.28
## 32 MtZoa+G(4)+I 65 -29722.89 59575.77 1.664165e-194 59576.89
## 27 mtArt+G(4) 64 -29727.75 59583.50 3.488603e-196 59584.59
## 28 mtArt+G(4)+I 65 -29728.06 59586.12 9.447127e-197 59587.23
## 39 VT+G(4) 64 -29742.01 59612.03 2.231969e-202 59613.11
## 19 cpREV+G(4) 64 -29743.66 59615.33 4.292618e-203 59616.41
## 40 VT+G(4)+I 65 -29741.98 59613.97 8.464233e-203 59615.09
## 18 cpREV+I 64 -29747.74 59623.49 7.242854e-205 59624.57
## 20 cpREV+G(4)+I 65 -29743.36 59616.72 2.134880e-203 59617.84
## 9 LG 63 -29752.74 59631.49 1.327548e-206 59632.54
## 59 Blosum62+G(4) 64 -29751.49 59630.97 1.718260e-206 59632.06
## 30 MtZoa+I 64 -29752.38 59632.76 7.041167e-207 59633.84
## 57 Blosum62 63 -29757.08 59640.17 1.730959e-208 59641.22
## 58 Blosum62+I 64 -29754.67 59637.34 7.099579e-208 59638.43
## 60 Blosum62+G(4)+I 65 -29751.51 59633.02 6.167908e-207 59634.14
## 38 VT+I 64 -29766.21 59660.42 6.931260e-213 59661.50
## 26 mtArt+I 64 -29775.88 59679.76 4.365891e-217 59680.85
## 37 VT 63 -29823.35 59772.69 2.888224e-237 59773.74
## 17 cpREV 63 -29824.29 59774.59 1.119339e-237 59775.64
## 51 HIVb+G(4) 64 -29854.96 59837.93 1.973936e-251 59839.01
## 52 HIVb+G(4)+I 65 -29854.39 59838.79 1.283383e-251 59839.91
## 50 HIVb+I 64 -29865.06 59858.11 8.168730e-256 59859.20
## 29 MtZoa 63 -29889.03 59904.06 8.591882e-266 59905.11
## 25 mtArt 63 -29955.98 60037.97 7.196560e-295 60039.02
## 49 HIVb 63 -29992.79 60111.59 7.422148e-311 60112.64
## 47 HIVw+G(4) 64 -30209.78 60547.56 0.000000e+00 60548.65
## 48 HIVw+G(4)+I 65 -30210.73 60551.46 0.000000e+00 60552.58
## 46 HIVw+I 64 -30236.56 60601.13 0.000000e+00 60602.21
## 55 FLU+G(4) 64 -30302.69 60733.38 0.000000e+00 60734.46
## 61 Dayhoff_DCMut 63 -30398.14 60922.28 0.000000e+00 60923.33
## 13 Dayhoff 63 -30401.82 60929.64 0.000000e+00 60930.69
## 62 Dayhoff_DCMut+I 64 -30398.14 60924.28 0.000000e+00 60925.37
## 63 Dayhoff_DCMut+G(4) 64 -30398.54 60925.08 0.000000e+00 60926.16
## 14 Dayhoff+I 64 -30401.82 60931.64 0.000000e+00 60932.72
## 15 Dayhoff+G(4) 64 -30402.21 60932.41 0.000000e+00 60933.50
## 64 Dayhoff_DCMut+G(4)+I 65 -30398.54 60927.08 0.000000e+00 60928.20
## 16 Dayhoff+G(4)+I 65 -30402.21 60934.41 0.000000e+00 60935.53
## 45 HIVw 63 -30422.04 60970.09 0.000000e+00 60971.14
## 23 mtmam+G(4) 64 -30715.03 61558.07 0.000000e+00 61559.15
## 22 mtmam+I 64 -30716.52 61561.05 0.000000e+00 61562.13
## 24 mtmam+G(4)+I 65 -30715.03 61560.05 0.000000e+00 61561.17
## 21 mtmam 63 -30756.67 61639.35 0.000000e+00 61640.40
## AICcw BIC
## 35 8.465957e-01 59128.79
## 36 1.534043e-01 59139.13
## 34 6.086313e-16 59198.53
## 33 1.636140e-60 59396.87
## 56 3.571382e-84 59519.67
## 54 4.010825e-86 59521.73
## 43 1.042388e-89 59538.24
## 44 3.749138e-90 59547.20
## 42 6.211082e-94 59557.69
## 41 3.968536e-113 59639.17
## 7 1.018837e-115 59658.02
## 8 3.619434e-116 59667.01
## 6 1.119092e-118 59671.65
## 67 3.123089e-123 59692.62
## 53 2.179213e-125 59695.63
## 68 1.109428e-123 59701.61
## 66 4.225951e-126 59705.83
## 5 3.138750e-140 59763.98
## 65 1.227880e-147 59798.09
## 11 2.165462e-177 59942.03
## 3 1.325889e-178 59947.62
## 12 7.808773e-178 59950.99
## 4 4.717135e-179 59956.60
## 2 8.112810e-181 59957.81
## 10 2.020110e-182 59965.20
## 1 4.623548e-192 60002.67
## 31 6.063632e-194 60018.26
## 32 1.640402e-194 60027.79
## 27 3.497785e-196 60028.57
## 28 9.312226e-197 60038.14
## 39 2.237843e-202 60057.09
## 19 4.303916e-203 60060.39
## 40 8.343368e-203 60065.99
## 18 7.261916e-205 60068.56
## 20 2.104395e-203 60068.74
## 9 1.353519e-206 60069.60
## 59 1.722782e-206 60076.04
## 30 7.059698e-207 60077.82
## 57 1.764822e-208 60078.28
## 58 7.118264e-208 60082.41
## 60 6.079833e-207 60085.04
## 38 6.949503e-213 60105.48
## 26 4.377381e-217 60124.83
## 37 2.944727e-237 60210.81
## 17 1.141237e-237 60212.70
## 51 1.979131e-251 60282.99
## 52 1.265056e-251 60290.81
## 50 8.190229e-256 60303.18
## 29 8.759968e-266 60342.18
## 25 7.337348e-295 60476.08
## 49 7.567350e-311 60549.70
## 47 0.000000e+00 60992.63
## 48 0.000000e+00 61003.48
## 46 0.000000e+00 61046.19
## 55 0.000000e+00 61178.44
## 61 0.000000e+00 61360.39
## 13 0.000000e+00 61367.75
## 62 0.000000e+00 61369.35
## 63 0.000000e+00 61370.15
## 14 0.000000e+00 61376.70
## 15 0.000000e+00 61377.48
## 64 0.000000e+00 61379.10
## 16 0.000000e+00 61386.43
## 45 0.000000e+00 61408.20
## 23 0.000000e+00 62003.13
## 22 0.000000e+00 62006.11
## 24 0.000000e+00 62012.07
## 21 0.000000e+00 62077.46Meilleur modele : mtREV24+G(4)
env$`mtREV24+G(4)`## pml(tree = `tree_mtREV24+G(4)`, data = data, model = "mtREV24",
## k = 4, shape = 0.552362280933957)Construction arbres
# Matrice de ditance
dm_aa_gr_ext_5 <- dist.ml(mySequences_align_aa_gr_ext_5_phangorn, model = "mtREV24")
# Construction arbre NJ
treeNJ_aa_gr_ext_5 <- NJ(dm_aa_gr_ext_5)Integration des parametres
fit_aa_gr_ext_5 = pml(treeNJ_aa_gr_ext_5, data=mySequences_align_aa_gr_ext_5_phangorn)
fitmtREV24_aa_gr_ext_5 <- update(fit_aa_gr_ext_5, model="mtREV24", shape = 0.55394324878572, k = 4)
fitmtREV24_aa_gr_ext_5 <- optim.pml(fitmtREV24_aa_gr_ext_5, model="mtREV24", optShape=TRUE, optGamma = TRUE,
rearrangement="stochastic", control=pml.control(trace=0))Analyse bootstrap avec correction
bs_aa_gr_ext_5 = bootstrap.pml(fitmtREV24_aa_gr_ext_5, multicore=FALSE, bs=1000, optNni=TRUE, control=pml.control(trace=0))
# Visualisation
plotBS(midpoint(fitmtREV24_aa_gr_ext_5$tree), bs_aa_gr_ext_5, p=0, type="p", frame="circle",
cex=0.6, bs.adj=c(0.5,0.5), bg="white")